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Chen S, Bi K, Liang H, Wu Z, Huang M, Chen X, Dong G, Sheng C. PROTAC derivatization of natural products for target identification and drug discovery: Design of evodiamine-based PROTACs as novel REXO4 degraders. J Adv Res 2024; 63:219-230. [PMID: 37913903 DOI: 10.1016/j.jare.2023.10.014] [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: 08/29/2023] [Revised: 10/18/2023] [Accepted: 10/28/2023] [Indexed: 11/03/2023] Open
Abstract
INTRODUCTION Natural products (NPs) play a crucial role in the development of therapeutic drugs. However, it is still highly challenging to identify the targets of NPs. Besides, NPs usually exert their pharmacological activities via acting on multiple targets or pathways, which also poses great difficulties for the target identification of NPs. OBJECTIVES Inspired by our continuous efforts in designing drug-like protein degraders, this study introduced a successful example for the target identification and drug discovery of natural products evodiamine by employing PROTAC technology. METHODS Taking advantages of proteolysis targeting chimera (PROTAC), herein an integrated strategy combining PROTAC derivatization, quantitative proteomic analysis and binding affinity validation was developed for target identification and drug discovery of antitumor NP evodiamine. RESULTS In this study, both highly potent PROTACs and negative controls were designed for quantitative proteomic analysis. Furthermore, REXO4 was confirmed as a direct target of 3-fluoro-10-hydroxylevodiamine, which induced cell death through ROS. In addition, the PROTAC 13c effectively degraded REXO4 both in vitro and in vivo, leading to potent antitumor activities and reduced toxic side effects. CONCLUSION In summary, we developed an integrated strategy for the target identification and drug discovery of NPs, which was successfully applied to the PROTAC derivatization and target characterization of evodiamine. This proof-of-concept study highlighted the superiority of PROTAC technology in target identification of NPs and accelerated the process of NPs-based drug discovery, exhibiting broad application in NP-based drug development.
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Affiliation(s)
- Shuqiang Chen
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, People's Republic of China.
| | - Kaijian Bi
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, People's Republic of China
| | - Huixin Liang
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, People's Republic of China
| | - Zhe Wu
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, People's Republic of China
| | - Min Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Xi Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, People's Republic of China
| | - Guoqiang Dong
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, People's Republic of China
| | - Chunquan Sheng
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, People's Republic of China.
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Farooqi AA, Rakhmetova V, Kapanova G, Tanbayeva G, Mussakhanova A, Abdykulova A, Ryskulova AG. Role of Ubiquitination and Epigenetics in the Regulation of AhR Signaling in Carcinogenesis and Metastasis: "Albatross around the Neck" or "Blessing in Disguise". Cells 2023; 12:2382. [PMID: 37830596 PMCID: PMC10571945 DOI: 10.3390/cells12192382] [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: 08/26/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
The molecular mechanisms and signal transduction cascades evoked by the activation of aryl hydrocarbon receptor (AhR) are becoming increasingly understandable. AhR is a ligand-activated transcriptional factor that integrates environmental, dietary and metabolic cues for the pleiotropic regulation of a wide variety of mechanisms. AhR mediates transcriptional programming in a ligand-specific, context-specific and cell-type-specific manner. Pioneering cutting-edge research works have provided fascinating new insights into the mechanistic role of AhR-driven downstream signaling in a wide variety of cancers. AhR ligands derived from food, environmental contaminants and intestinal microbiota strategically activated AhR signaling and regulated multiple stages of cancer. Although AhR has classically been viewed and characterized as a ligand-regulated transcriptional factor, its role as a ubiquitin ligase is fascinating. Accordingly, recent evidence has paradigmatically shifted our understanding and urged researchers to drill down deep into these novel and clinically valuable facets of AhR biology. Our rapidly increasing realization related to AhR-mediated regulation of the ubiquitination and proteasomal degradation of different proteins has started to scratch the surface of intriguing mechanisms. Furthermore, AhR and epigenome dynamics have shown previously unprecedented complexity during multiple stages of cancer progression. AhR not only transcriptionally regulated epigenetic-associated molecules, but also worked with epigenetic-modifying enzymes during cancer progression. In this review, we have summarized the findings obtained not only from cell-culture studies, but also from animal models. Different clinical trials are currently being conducted using AhR inhibitors and PD-1 inhibitors (Pembrolizumab and nivolumab), which confirm the linchpin role of AhR-related mechanistic details in cancer progression. Therefore, further studies are required to develop a better comprehension of the many-sided and "diametrically opposed" roles of AhR in the regulation of carcinogenesis and metastatic spread of cancer cells to the secondary organs.
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Affiliation(s)
- Ammad Ahmad Farooqi
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad 54000, Pakistan
| | - Venera Rakhmetova
- Department of Internal Diseases, Medical University of Astana, Astana 010000, Kazakhstan
| | - Gulnara Kapanova
- Faculty of Medicine and healthcare, Al-Farabi Kazakh National University, 71 Al-Farabi Ave, Almaty 050040, Kazakhstan (G.T.)
- Scientific Center of Anti-Infectious Drugs, 75 Al-Farabi Ave, Almaty 050040, Kazakhstan
| | - Gulnur Tanbayeva
- Faculty of Medicine and healthcare, Al-Farabi Kazakh National University, 71 Al-Farabi Ave, Almaty 050040, Kazakhstan (G.T.)
| | - Akmaral Mussakhanova
- Department of Public Health and Management, Astana Medical University, Astana 010000, Kazakhstan;
| | - Akmaral Abdykulova
- Department of General Medical Practice, General Medicine Faculty, Asfendiyarov Kazakh National Medical University, Almaty 050000, Kazakhstan;
| | - Alma-Gul Ryskulova
- Department of Public Health and Social Sciences, Kazakhstan Medical University “KSPH”, Utenos Str. 19A, Almaty 050060, Kazakhstan;
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Silva JL, Foguel D, Ferreira VF, Vieira TCRG, Marques MA, Ferretti GDS, Outeiro TF, Cordeiro Y, de Oliveira GAP. Targeting Biomolecular Condensation and Protein Aggregation against Cancer. Chem Rev 2023. [PMID: 37379327 DOI: 10.1021/acs.chemrev.3c00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Biomolecular condensates, membrane-less entities arising from liquid-liquid phase separation, hold dichotomous roles in health and disease. Alongside their physiological functions, these condensates can transition to a solid phase, producing amyloid-like structures implicated in degenerative diseases and cancer. This review thoroughly examines the dual nature of biomolecular condensates, spotlighting their role in cancer, particularly concerning the p53 tumor suppressor. Given that over half of the malignant tumors possess mutations in the TP53 gene, this topic carries profound implications for future cancer treatment strategies. Notably, p53 not only misfolds but also forms biomolecular condensates and aggregates analogous to other protein-based amyloids, thus significantly influencing cancer progression through loss-of-function, negative dominance, and gain-of-function pathways. The exact molecular mechanisms underpinning the gain-of-function in mutant p53 remain elusive. However, cofactors like nucleic acids and glycosaminoglycans are known to be critical players in this intersection between diseases. Importantly, we reveal that molecules capable of inhibiting mutant p53 aggregation can curtail tumor proliferation and migration. Hence, targeting phase transitions to solid-like amorphous and amyloid-like states of mutant p53 offers a promising direction for innovative cancer diagnostics and therapeutics.
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Affiliation(s)
- Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Debora Foguel
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Vitor F Ferreira
- Faculty of Pharmacy, Fluminense Federal University (UFF), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tuane C R G Vieira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Giulia D S Ferretti
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center, 37075 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH, U.K
- Scientific employee with an honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 37075 Göttingen, Germany
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
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Sondermann NC, Faßbender S, Hartung F, Hätälä AM, Rolfes KM, Vogel CFA, Haarmann-Stemmann T. Functions of the aryl hydrocarbon receptor (AHR) beyond the canonical AHR/ARNT signaling pathway. Biochem Pharmacol 2023; 208:115371. [PMID: 36528068 PMCID: PMC9884176 DOI: 10.1016/j.bcp.2022.115371] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022]
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor regulating adaptive and maladaptive responses toward exogenous and endogenous signals. Research from various biomedical disciplines has provided compelling evidence that the AHR is critically involved in the pathogenesis of a variety of diseases and disorders, including autoimmunity, inflammatory diseases, endocrine disruption, premature aging and cancer. Accordingly, AHR is considered an attractive target for the development of novel preventive and therapeutic measures. However, the ligand-based targeting of AHR is considerably complicated by the fact that the receptor does not always follow the beaten track, i.e. the canonical AHR/ARNT signaling pathway. Instead, AHR might team up with other transcription factors and signaling molecules to shape gene expression patterns and associated physiological or pathophysiological functions in a ligand-, cell- and micromilieu-dependent manner. Herein, we provide an overview about some of the most important non-canonical functions of AHR, including crosstalk with major signaling pathways involved in controlling cell fate and function, immune responses, adaptation to low oxygen levels and oxidative stress, ubiquitination and proteasomal degradation. Further research on these diverse and exciting yet often ambivalent facets of AHR biology is urgently needed in order to exploit the full potential of AHR modulation for disease prevention and treatment.
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Affiliation(s)
- Natalie C Sondermann
- IUF - Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Sonja Faßbender
- IUF - Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Frederick Hartung
- IUF - Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Anna M Hätälä
- IUF - Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Katharina M Rolfes
- IUF - Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Christoph F A Vogel
- Department of Environmental Toxicology and Center for Health and the Environment, University of California, Davis, CA 95616, USA
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5
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Alqahtani MA, El-Ghiaty MA, El-Kadi AOS. Mercury and methylmercury differentially modulate hepatic cytochrome P450 1A1 and 1A2 in vivo and in vitro. J Biochem Mol Toxicol 2023; 37:e23243. [PMID: 36245390 DOI: 10.1002/jbt.23243] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 08/16/2022] [Accepted: 10/06/2022] [Indexed: 11/08/2022]
Abstract
The cytochrome P450 1 A (CYP1A) subfamily enzymes are involved in the metabolic activation of several xenobiotics to toxic metabolites and reactive intermediates, resulting ultimately in carcinogenesis. Mercury and halogenated aromatic hydrocarbons (HAHs), typified by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), are persistent environmental pollutants involved in the modulation of aryl hydrocarbon receptor (AHR) gene battery, including cytochrome P450 (CYP) genes. We previously investigated the effect of coexposure to either inorganic or organic mercury (Hg+2 and MeHg) with TCDD on CYP1A1 in vitro. Thus, we examined the impact of coexposure to Hg+2 or MeHg and TCDD on AHR-regulated genes (Cyp1a1/1a2) in vivo and in vitro. Therefore, male C57BL/6 mice were injected intraperitoneally with MeHg or Hg+2 (2.5 mg/kg) in the absence and presence of TCDD (15 μg/kg) for 6 or 24 h. The concentration-dependent effect of MeHg was examined in murine hepatoma Hepa1c1c7 cells. In vivo, both MeHg and Hg2+ inhibited the TCDD-mediated induction of Cyp1a1/1a2 mRNA levels. However, Only Hg2+ was able to inhibit the TCDD-mediated induction at posttranscriptional levels of CYP1A1/1A2 protein and catalytic activity, suggesting differential modulation effects by Hg+2 and MeHg. In addition, the inhibitory role of HO-1 (Heme oxygenase-1) on CYP1A activity induced by TCDD was investigated using a HO-1 competitive inhibitor, tin-mesoporphyrin, that partially restored the MeHg-mediated decrease in CYP1A1 activity. This study demonstrates that MeHg, alongside Hg2+ , can differentially modulate the TCDD-induced AHR-regulated genes (Cyp1a1/1a2) at different expression levels in C57BL/6 mice liver and Hepa1c1c7 cells.
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Affiliation(s)
- Mohammed A Alqahtani
- Department of Pharmaceutical Sciences, 2142 J Katz Group-Rexall Centre for Pharmacy and Health Research Edmonton, University of Alberta Ringgold Standard Institution, Edmonton, Alberta, Canada
| | - Mahmoud A El-Ghiaty
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Ayman O S El-Kadi
- Faculty of Pharmacy and Pharmaceutical Sciences, 2142 J Katz Group-Rexall Centre for Pharmacy and Health Research, University of Alberta, Edmonton, Alberta, Canada
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6
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Zhao HY, Xin M, Zhang SQ. Progress of small molecules for targeted protein degradation: PROTACs and other technologies. Drug Dev Res 2023; 84:337-394. [PMID: 36606428 DOI: 10.1002/ddr.22026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/01/2022] [Accepted: 12/17/2022] [Indexed: 01/07/2023]
Abstract
Recent years have witnessed the rapid development of targeted protein degradation (TPD), especially proteolysis targeting chimeras. These degraders have manifested many advantages over small molecule inhibitors. To date, a huge number of degraders have been excavated against over 70 disease-related targets. In particular, degraders against estrogen receptor and androgen receptor have crowded into phase II clinical trial. TPD technologies largely expand the scope of druggable targets, and provide powerful tools for addressing intractable problems that can not be tackled by traditional small molecule inhibitors. In this review, we mainly focus on the structures and biological activities of small molecule degraders as well as the elucidation of mechanisms of emerging TPD technologies. We also propose the challenges that exist in the TPD field at present.
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Affiliation(s)
- Hong-Yi Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Minhang Xin
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - San-Qi Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
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7
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Chatterjee DR, Kapoor S, Jain M, Das R, Chowdhury MG, Shard A. PROTACting the kinome with covalent warheads. Drug Discov Today 2023; 28:103417. [PMID: 36306996 DOI: 10.1016/j.drudis.2022.103417] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/19/2022] [Accepted: 10/19/2022] [Indexed: 02/02/2023]
Abstract
The dawn of targeted degradation using proteolysis-targeting chimeras (PROTACs) against recalcitrant proteins has prompted numerous efforts to develop complementary drugs. Although many of these are specifically directed against undruggable proteins, there is increasing interest in small molecule-based PROTACs that target intracellular pathways, and some have recently entered clinical trials. Concurrently, small molecule-based PROTACs that target protumorigenic pathways in cancer cells, the tumor microenvironment (TME), and angiogenesis have been found to have potent effects that synergize with the action of antibodies. This has led to the augmentation of PROTACs with variable substitution patterns. Several combinations with small molecules targeting undruggable proteins are now under clinical investigation. In this review, we discuss the recent milestones achieved as well as challenges encountered in this area of drug development, as well as our opinion on the best path forward.
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Affiliation(s)
- Deep Rohan Chatterjee
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Saumya Kapoor
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Meenakshi Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Moumita Ghosh Chowdhury
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India.
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Kim S, Lim SW, Choi J. Drug discovery inspired by bioactive small molecules from nature. Anim Cells Syst (Seoul) 2022; 26:254-265. [PMID: 36605590 PMCID: PMC9809404 DOI: 10.1080/19768354.2022.2157480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Natural products (NPs) have greatly contributed to the development of novel treatments for human diseases such as cancer, metabolic disorders, and infections. Compared to synthetic chemical compounds, primary and secondary metabolites from medicinal plants, fungi, microorganisms, and our bodies are promising resources with immense chemical diversity and favorable properties for drug development. In addition to the well-validated significance of secondary metabolites, endogenous small molecules derived from central metabolism and signaling events have shown great potential as drug candidates due to their unique metabolite-protein interactions. In this short review, we highlight the values of NPs, discuss recent scientific and technological advances including metabolomics tools, chemoproteomics approaches, and artificial intelligence-based computation platforms, and explore potential strategies to overcome the current challenges in NP-driven drug discovery.
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Affiliation(s)
- Seyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea, Seyun Kim
| | - Seol-Wa Lim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jiyeon Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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Liu M, Martyn AP, Quinn RJ. Natural product-based PROteolysis TArgeting Chimeras (PROTACs). Nat Prod Rep 2022; 39:2292-2307. [PMID: 36196977 DOI: 10.1039/d2np00038e] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: upto 2022Natural products have an embedded recognition of protein surfaces. They possess this property as they are produced by biosynthetic enzymes and are substrates for one or more enzymes in the biosynthetic pathway. The inherent advantages, compared to synthetic compound libraries, is this ligand-protein binding which is, in many cases, a function of the 3-dimensional properties. Protein degradation is a recent novel therapeutic approach with several compounds now in the clinic. This review highlights the potential of PROteolysis TArgeting Chimeras (PROTACs) in the area of natural products. The approach will complement existing approaches such as the direct use of a bioactive natural product or its analogues, pharmacophore development and drug-antibody conjugates. The chemical synthesis and challenges of using natural product-based PROTACs are summarised. The review also highlights methods to detect the ternary complexes necessary for PROTAC mechanism of action.
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Affiliation(s)
- Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
| | - Alexander P Martyn
- Cancer and Ageing Research Program (CARP), Centre for Genomics and Personalised Health (CGPH), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
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Palacios DS. Drug Hunting at the Nexus of Medicinal Chemistry and Chemical Biology and the Discovery of Novel Therapeutic Modalities. J Med Chem 2022; 65:13594-13613. [PMID: 36206538 DOI: 10.1021/acs.jmedchem.2c01491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small molecules designed to modulate protein function have been remarkably successful in advancing human health. As the frontiers of medicine and understanding of disease pathogenesis continue to expand, small molecule scientists must also pursue the development of novel therapeutic modalities beyond functional protein modulation to address diseases of unmet medical need. In this vein, this Perspective will highlight two emerging modalities, selective mRNA splice modulation and targeted protein degradation, as mechanisms that affect protein abundance, rather than protein function, to broaden the scope of low-molecular-weight treatable diseases. Key to the elucidation and development of these mechanisms was the interplay and contemporaneous efforts in medicinal chemistry and chemical biology. Continued research at the intersection of these two fields will be critical for the identification of novel targets and mechanisms toward the development of the next generation of small molecule therapeutics.
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Affiliation(s)
- Daniel S Palacios
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
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Current Therapeutic Landscape and Safety Roadmap for Targeting the Aryl Hydrocarbon Receptor in Inflammatory Gastrointestinal Indications. Cells 2022; 11:cells11101708. [PMID: 35626744 PMCID: PMC9139855 DOI: 10.3390/cells11101708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/30/2022] [Accepted: 05/16/2022] [Indexed: 02/07/2023] Open
Abstract
Target modulation of the AhR for inflammatory gastrointestinal (GI) conditions holds great promise but also the potential for safety liabilities both within and beyond the GI tract. The ubiquitous expression of the AhR across mammalian tissues coupled with its role in diverse signaling pathways makes development of a “clean” AhR therapeutically challenging. Ligand promiscuity and diversity in context-specific AhR activation further complicates targeting the AhR for drug development due to limitations surrounding clinical translatability. Despite these concerns, several approaches to target the AhR have been explored such as small molecules, microbials, PROTACs, and oligonucleotide-based approaches. These various chemical modalities are not without safety liabilities and require unique de-risking strategies to parse out toxicities. Collectively, these programs can benefit from in silico and in vitro methodologies that investigate specific AhR pathway activation and have the potential to implement thresholding parameters to categorize AhR ligands as “high” or “low” risk for sustained AhR activation. Exploration into transcriptomic signatures for AhR safety assessment, incorporation of physiologically-relevant in vitro model systems, and investigation into chronic activation of the AhR by structurally diverse ligands will help address gaps in our understanding regarding AhR-dependent toxicities. Here, we review the role of the AhR within the GI tract, novel therapeutic modality approaches to target the AhR, key AhR-dependent safety liabilities, and relevant strategies that can be implemented to address drug safety concerns. Together, this review discusses the emerging therapeutic landscape of modalities targeting the AhR for inflammatory GI indications and offers a safety roadmap for AhR drug development.
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Ma Z, Ji Y, Yu Y, Liang D. Specific non-genetic IAP-based protein erasers (SNIPERs) as a potential therapeutic strategy. Eur J Med Chem 2021; 216:113247. [PMID: 33652355 DOI: 10.1016/j.ejmech.2021.113247] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/13/2021] [Accepted: 01/25/2021] [Indexed: 12/29/2022]
Abstract
As a newly emerged technology, PROTAC (proteolysis targeting chimera) is a promising therapeutic strategy for varieties of diseases. Unlike small molecule inhibitors, PROTACs catalytically induce target proteins degradation, including currently "undruggable" target proteins. In addition, PROTACs can be a potentially successful strategy to overcome drug resistance. IAPs can inhibit apoptosis by inhibiting caspase, and also exhibits the activity of E3 ubiquitin ligase. Specific and nongenetic IAP-based protein erasers (SNIPERs) are hybrid molecules that designed based on IAPs, and used to degrade the target proteins closely associated with diseases. Their structures consist of three parts, including target protein ligand, E3 ligase ligand and the linker between them. SNIPERs (PROTACs) degrade diseases-associated proteins through human inherent ubiquitin-proteasome system. So far, many SNIPERs have been developed to treat diseases that difficult to handle by traditional methods, such as radiotherapy, chemotherapy and small molecule inhibitors, and showed promising prospects in application. In this paper, the recent advances of SNIPERs were summarized, and the chances and challenges associated with this area were also highlighted.
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Affiliation(s)
- Zonghui Ma
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China.
| | - Yu Ji
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China
| | - Yifan Yu
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China
| | - Dailin Liang
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China
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The Potential of Proteolytic Chimeras as Pharmacological Tools and Therapeutic Agents. Molecules 2020; 25:molecules25245956. [PMID: 33339292 PMCID: PMC7766482 DOI: 10.3390/molecules25245956] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/09/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
The induction of protein degradation in a highly selective and efficient way by means of druggable molecules is known as targeted protein degradation (TPD). TPD emerged in the literature as a revolutionary idea: a heterobifunctional chimera with the capacity of creating an interaction between a protein of interest (POI) and a E3 ubiquitin ligase will induce a process of events in the POI, including ubiquitination, targeting to the proteasome, proteolysis and functional silencing, acting as a sort of degradative knockdown. With this programmed protein degradation, toxic and disease-causing proteins could be depleted from cells with potentially effective low drug doses. The proof-of-principle validation of this hypothesis in many studies has made the TPD strategy become a new attractive paradigm for the development of therapies for the treatment of multiple unmet diseases. Indeed, since the initial protacs (Proteolysis targeting chimeras) were posited in the 2000s, the TPD field has expanded extraordinarily, developing innovative chemistry and exploiting multiple degradation approaches. In this article, we review the breakthroughs and recent novel concepts in this highly active discipline.
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14
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Bao SM, Hu QH, Yang WT, Wang Y, Tong YP, Bao WD. Targeting Epidermal Growth Factor Receptor in Non-Small-Cell-Lung Cancer: Current State and Future Perspective. Anticancer Agents Med Chem 2020; 19:984-991. [PMID: 30868964 DOI: 10.2174/1871520619666190313161009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 12/20/2018] [Accepted: 03/01/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Lung cancer is one of the leading cause of cancer death worldwide, the most common histological type of lung cancer is non-small cell lung cancer (NSCLC), whose occurrence and development is closely related to the mutation and amplification of epidermal growth factor receptors (EGFR). Currently , a series of targeted drugs were developed on the inhibition of EGFR such as epidermal growth factor receptortyrosine kinase inhibitor EGFR-TKI and monoclonal antibody (McAb). OBJECTIVE We sought to summarizes the current drugs targeting Epidermal Growth Factor Receptor in nonsmall- cell-lung. METHODS We conducted a comprehensive review of the development and application of EGFR-TKI and McAb which targeted EGFR in NSCLC and compared the mechanisms of PROTAC with the traditional inhibitors. RESULTS The drugs targeted EGFR in NSCLC have been widely used in clinic practices. Compared to traditional chemotherapy, these drugs excel with their clear and specific targeting, better curative effects, and less toxic and side effects. However, the mechanism comes with some insurmountable weaknesses like serious toxic and other side effects, as well as proneness to producing drug resistance. CONCLUSION The emerging PROTAC (Proteolysis Targeting Chimera) technology has been successfully applied to selective degradation of multiple protein targets, including EGFR. It also highlights the potential and challenges of PROTAC therapy regarding future combination therapeutic options in NSCLC treatment.
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Affiliation(s)
- Shui-Ming Bao
- Department of biology, East China University of Technology, 418 Guanglan Road, Nan chang, Jiangxi province 330013, China
| | - Qing-Hui Hu
- Nanchang Five Elements Biology Technology Company Limited, Nanchang, Jiangxi, China
| | - Wen-Ting Yang
- Nanchang Five Elements Biology Technology Company Limited, Nanchang, Jiangxi, China
| | - Yao Wang
- Nanchang Five Elements Biology Technology Company Limited, Nanchang, Jiangxi, China
| | - Yin-Ping Tong
- Nanchang Five Elements Biology Technology Company Limited, Nanchang, Jiangxi, China
| | - Wen-Dai Bao
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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15
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Scheepstra M, Hekking KF, van Hijfte L, Folmer RH. Bivalent Ligands for Protein Degradation in Drug Discovery. Comput Struct Biotechnol J 2019; 17:160-176. [PMID: 30788082 PMCID: PMC6369262 DOI: 10.1016/j.csbj.2019.01.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/16/2019] [Accepted: 01/19/2019] [Indexed: 01/19/2023] Open
Abstract
Targeting the "undruggable" proteome remains one of the big challenges in drug discovery. Recent innovations in the field of targeted protein degradation and manipulation of the ubiquitin-proteasome system open up new therapeutic approaches for disorders that cannot be targeted with conventional inhibitor paradigms. Proteolysis targeting chimeras (PROTACs) are bivalent ligands in which a compound that binds to the protein target of interest is connected to a second molecule that binds an E3 ligase via a linker. The E3 protein is usually either Cereblon or Von Hippel-Lindau. Several examples of selective PROTAC molecules with potent effect in cells and in vivo models have been reported. The degradation of specific proteins via these bivalent molecules is already allowing for the study of biochemical pathways and cell biology with more specificity than was possible with inhibitor compounds. In this review, we provide a comprehensive overview of recent developments in the field of small molecule mediated protein degradation, including transcription factors, kinases and nuclear receptors. We discuss the potential benefits of protein degradation over inhibition as well as the challenges that need to be overcome.
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Key Words
- ABCB1, ATP-binding cassette sub-family B member 1
- AD, Alzheimer's disease
- AHR, aryl hydrogen receptor
- ALK, anaplastic lymphoma kinase
- Aβ, amyloid-β
- BET, bromodomain and extra-terminal
- BTK, Bruton's tyrosine kinase
- Bcl6, B-cell lymphoma 6
- Bivalent ligand
- Brd4, bromodomain 4
- CDK9, cyclin dependent kinase 9
- CK2, Casein kinase 2
- CLIPTAC, click-formed proteolysis targeting chimera
- CRBN, Cereblon
- Chimera
- DC50, the compound concentration that results in 50% target protein degradation
- DHODH, Dihydroorotate dehydrogenase
- Degrader
- ERK1, extracellular signal-regulated kinase 1
- ERRα, estrogen-related receptor alpha
- ERα, estrogen receptor alpha
- EZH2, enhancer of zeste homolog 2
- FLT3, FMS-like tyrosine kinase-3
- FRS2, fibroblast growth factor receptor substrate 2
- GCN5, general control nonderepressible 5
- GPCR, G-protein coupled receptor
- GST, glutathione S-transferase
- HDAC, histone deacetylase
- HTS, high-throughput screening
- MDM2, mouse double-minute 2 homolog
- MetAP-2, methionine aminopeptidase-2
- PCAF, P300/CBP-associated factor
- PEG, polyethylene glycol
- PI3K, phosphatidylinositol-3-kinase
- PLK-1, polo-like kinase 1
- POI, protein of interest
- PROTAC
- PROTAC, proteolysis targeting chimeras
- Proteasome
- Protein degradation
- RAR, retinoic acid receptor
- RIPK2, receptor-interacting serine/threonine-protein kinase 2
- RTK, receptor tyrosine kinase
- SARM, selective androgen receptor modulator
- SNIPER, specific and non-genetic IAP-dependent protein eraser
- TBK1, TANK-Binding kinase 1
- TRIM24, tripartite motif-containing 24 (also known as TIF1α)
- VHL, Von Hippel-Lindau
- cIAP1, cellular inhibitor of apoptosis protein
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16
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Zou Y, Ma D, Wang Y. The PROTAC technology in drug development. Cell Biochem Funct 2019; 37:21-30. [PMID: 30604499 PMCID: PMC6590639 DOI: 10.1002/cbf.3369] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/28/2022]
Abstract
Currently, a new technology termed PROTAC, proteolysis targeting chimera, has been developed for inducing the protein degradation by a targeting molecule. This technology takes advantage of a moiety of targeted protein and a moiety of recognizing E3 ubiquitin ligase and produces a hybrid molecule to specifically knock down a targeted protein. During the first decade, three pedigreed groups worked on the development of this technology. To date, this technology has been extended by different groups, aiming to develop new drugs against different diseases including cancers. This review summarizes the contributions of the groups for the development of PROTAC. SIGNIFICANCE OF THE STUDY: This review summarized the development of the PROTAC technology for readers and also presented the author's opinions on the application of the technology in tumor therapy.
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Affiliation(s)
- Yutian Zou
- The State Laboratory of Membrane Biology, Department of Basic Medicine, School of Medicine, Tsinghua University, Beijing, China.,Department of Science, Brookwood High School, Snellville, Georgia
| | - Danhui Ma
- The State Laboratory of Membrane Biology, Department of Basic Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Yinyin Wang
- The State Laboratory of Membrane Biology, Department of Basic Medicine, School of Medicine, Tsinghua University, Beijing, China
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17
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Hines J, Lartigue S, Dong H, Qian Y, Crews CM. MDM2-Recruiting PROTAC Offers Superior, Synergistic Antiproliferative Activity via Simultaneous Degradation of BRD4 and Stabilization of p53. Cancer Res 2019; 79:251-262. [PMID: 30385614 PMCID: PMC6318015 DOI: 10.1158/0008-5472.can-18-2918] [Citation(s) in RCA: 211] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 12/20/2022]
Abstract
Although the number of proteins effectively targeted for posttranslational degradation by PROTAC has grown steadily, the number of E3 ligases successfully exploited to accomplish this has been limited to the few for which small-molecule ligands have been discovered. Although the E3 ligase MDM2 is bound by the nutlin class of small-molecule ligands, there are few nutlin-based PROTAC. Because a nutlin-based PROTAC should both knockdown its target protein and upregulate the tumor suppressor p53, we examined the ability of such a PROTAC to decrease cancer cell viability. A nutlin-based, BRD4-degrading PROTAC, A1874, was able to degrade its target protein by 98% with nanomolar potency. Given the complementary ability of A1874 to stabilize p53, we discovered that the nutlin-based PROTAC was more effective in inhibiting proliferation of many cancer cell lines with wild-type p53 than was a corresponding VHL-utilizing PROTAC with similar potency and efficacy to degrade BRD4. This is the first report of a PROTAC in which the E3 ligase ligand and targeting warhead combine to exert a synergistic antiproliferative effect. Our study highlights the untapped potential that may be unlocked by expanding the repertoire of E3 ligases that can be recruited by PROTAC. SIGNIFICANCE: These findings present the first BRD4-targeting MDM2-based PROTAC that possesses potent, distinct, and synergistic biological activities associated with both ends of this heterobifunctional molecule.
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Affiliation(s)
- John Hines
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut
| | - Schan Lartigue
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut
| | | | | | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut.
- Department of Chemistry, Yale University, New Haven, Connecticut
- Department of Pharmacology, Yale University, New Haven, Connecticut
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18
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Cheng J, Guo J, North BJ, Tao K, Zhou P, Wei W. The emerging role for Cullin 4 family of E3 ligases in tumorigenesis. Biochim Biophys Acta Rev Cancer 2018; 1871:138-159. [PMID: 30602127 DOI: 10.1016/j.bbcan.2018.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
As a member of the Cullin-RING ligase family, Cullin-RING ligase 4 (CRL4) has drawn much attention due to its broad regulatory roles under physiological and pathological conditions, especially in neoplastic events. Based on evidence from knockout and transgenic mouse models, human clinical data, and biochemical interactions, we summarize the distinct roles of the CRL4 E3 ligase complexes in tumorigenesis, which appears to be tissue- and context-dependent. Notably, targeting CRL4 has recently emerged as a noval anti-cancer strategy, including thalidomide and its derivatives that bind to the substrate recognition receptor cereblon (CRBN), and anticancer sulfonamides that target DCAF15 to suppress the neoplastic proliferation of multiple myeloma and colorectal cancers, respectively. To this end, PROTACs have been developed as a group of engineered bi-functional chemical glues that induce the ubiquitination-mediated degradation of substrates via recruiting E3 ligases, such as CRL4 (CRBN) and CRL2 (pVHL). We summarize the recent major advances in the CRL4 research field towards understanding its involvement in tumorigenesis and further discuss its clinical implications. The anti-tumor effects using the PROTAC approach to target the degradation of undruggable targets are also highlighted.
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Affiliation(s)
- Ji Cheng
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Brian J North
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Pengbo Zhou
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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19
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Shibata N, Shimokawa K, Nagai K, Ohoka N, Hattori T, Miyamoto N, Ujikawa O, Sameshima T, Nara H, Cho N, Naito M. Pharmacological difference between degrader and inhibitor against oncogenic BCR-ABL kinase. Sci Rep 2018; 8:13549. [PMID: 30202081 PMCID: PMC6131351 DOI: 10.1038/s41598-018-31913-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/29/2018] [Indexed: 01/09/2023] Open
Abstract
Chronic myelogenous leukemia (CML) is characterized by the oncogenic fusion protein, BCR-ABL protein kinase, against which clinically useful inhibitors have been developed. An alternative approach to treat CML is to degrade the BCR-ABL protein. Recently, potent degraders against BCR-ABL have been developed by conjugating dasatinib to ligands for E3 ubiquitin ligases. Since the degraders contain the dasatinib moiety, they also inhibit BCR-ABL kinase activity, which complicates our understanding of the impact of BCR-ABL degradation by degraders in CML growth inhibition. To address this issue, we chose DAS-IAP, as a potent BCR-ABL degrader, and developed a structurally related inactive degrader, DAS-meIAP, which inhibits kinase activity but does not degrade the BCR-ABL protein. DAS-IAP showed slightly weaker activity than DAS-meIAP in inhibiting cell growth when CML cells were treated for 48 h. However, DAS-IAP showed sustained growth inhibition even when the drug was removed after short-term treatment, whereas CML cell growth rapidly resumed following removal of DAS-meIAP and dasatinib. Consistently, suppression of BCR-ABL levels and downstream kinase signaling were maintained after DAS-IAP removal, whereas kinase signaling rapidly recovered following removal of DAS-meIAP and dasatinib. These results indicate that BCR-ABL degrader shows more sustained inhibition of CML cell growth than ABL kinase inhibitor.
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Affiliation(s)
- Norihito Shibata
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Kenichiro Shimokawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Katsunori Nagai
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan.,Axcelead Drug Discovery Partners, Inc., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-0012, Japan
| | - Nobumichi Ohoka
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takayuki Hattori
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Naoki Miyamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Osamu Ujikawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan.,Axcelead Drug Discovery Partners, Inc., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-0012, Japan
| | - Tomoya Sameshima
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hiroshi Nara
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan.,The Pharmaceutical Society of Japan, 2-12-15 Shibuya, Shibuya-ku, Tokyo, 150-0002, Japan
| | - Nobuo Cho
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan.,Drug Discovery Chemistry Platform Unit (Wako branch), RIKEN Center for Life Science Technologies, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Mikihiko Naito
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan.
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20
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Cermakova K, Hodges HC. Next-Generation Drugs and Probes for Chromatin Biology: From Targeted Protein Degradation to Phase Separation. Molecules 2018; 23:molecules23081958. [PMID: 30082609 PMCID: PMC6102721 DOI: 10.3390/molecules23081958] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/01/2018] [Accepted: 08/01/2018] [Indexed: 12/31/2022] Open
Abstract
Chromatin regulation is a critical aspect of nuclear function. Recent advances have provided detailed information about dynamic three-dimensional organization of chromatin and its regulatory factors. Mechanisms crucial for normal nuclear function and epigenetic control include compartmentalization of biochemical reactions by liquid-phase separated condensates and signal-dependent regulation of protein stability. Synthetic control of these phenomena by small molecules provides deep insight into essential activities such as histone modification, BAF (SWI/SNF) and PBAF remodeling, Polycomb repression, enhancer looping by cohesin and CTCF, as well as many other processes that contribute to transcription. As a result, a complete understanding of the spatiotemporal mechanisms that underlie chromatin regulation increasingly requires the use of fast-acting drugs and chemical probes. Here, we provide a comprehensive review of next-generation chemical biology tools to interrogate the chromatin regulatory landscape, including selective PROTAC E3 ubiquitin ligase degraders, degrons, fluorescent ligands, dimerizers, inhibitors, and other drugs. These small molecules provide important insights into the mechanisms that govern gene regulation, DNA repair, development, and diseases like cancer.
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Affiliation(s)
- Katerina Cermakova
- Department of Molecular & Cellular Biology, Center for Precision Environmental Health, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - H Courtney Hodges
- Department of Molecular & Cellular Biology, Center for Precision Environmental Health, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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21
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Simple and efficient knockdown of His-tagged proteins by ternary molecules consisting of a His-tag ligand, a ubiquitin ligase ligand, and a cell-penetrating peptide. Bioorg Med Chem Lett 2017; 27:4478-4481. [PMID: 28807436 DOI: 10.1016/j.bmcl.2017.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 11/22/2022]
Abstract
We designed and synthesized hybrid molecules for a protein knockdown method based on the recognition of a His-tag fused to a protein of interest (POI). The synthesized target protein degradation inducers contained three functional moieties: a His-tag ligand (nickel nitrilotriacetic acid [Ni-NTA]), an E3 ligand (bestatin [BS] or MV1), and a carrier peptide (Tat or nonaarginine [R9]). The designed hybrid molecules, BS-Tat-Ni-NTA, MV1-Tat-Ni-NTA, BS-R9-Ni-NTA, and MV1-R9-Ni-NTA, efficiently degraded His-tagged cellular retinoic acid binding protein 2 via the ubiquitin-proteasome system (UPS). This system will become a useful tool for research into selective protein degradation inducers that act via the UPS.
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22
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Shibata N, Nagai K, Morita Y, Ujikawa O, Ohoka N, Hattori T, Koyama R, Sano O, Imaeda Y, Nara H, Cho N, Naito M. Development of Protein Degradation Inducers of Androgen Receptor by Conjugation of Androgen Receptor Ligands and Inhibitor of Apoptosis Protein Ligands. J Med Chem 2017; 61:543-575. [DOI: 10.1021/acs.jmedchem.7b00168] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Norihito Shibata
- Divisions
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Katsunori Nagai
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Yoko Morita
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Osamu Ujikawa
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Nobumichi Ohoka
- Divisions
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Takayuki Hattori
- Divisions
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Ryokichi Koyama
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Osamu Sano
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Yasuhiro Imaeda
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Hiroshi Nara
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Nobuo Cho
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Mikihiko Naito
- Divisions
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
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23
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Abstract
Traditional pharmaceutical drug discovery is almost exclusively focused on directly controlling protein activity to cure diseases. Modulators of protein activity, especially inhibitors, are developed and applied at high concentration to achieve maximal effects. Thereby, reduced bioavailability and off-target effects can hamper compound efficacy. Nucleic acid-based strategies that control protein function by affecting expression have emerged as an alternative. However, metabolic stability and broad bioavailability represent development hurdles that remain to be overcome for these approaches. More recently, utilizing the cell's own protein destruction machinery for selective degradation of essential drivers of human disorders has opened up a new and exciting area of drug discovery. Small-molecule-induced proteolysis of selected substrates offers the potential of reaching beyond the limitations of the current pharmaceutical paradigm to expand the druggable target space.
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Affiliation(s)
- Philipp M Cromm
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06511, USA.
| | - Craig M Crews
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06511, USA; Department of Chemistry, Yale University, New Haven, CT 06511, USA; Department of Pharmacology, Yale University, New Haven, CT 06511, USA.
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24
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Shibata N, Miyamoto N, Nagai K, Shimokawa K, Sameshima T, Ohoka N, Hattori T, Imaeda Y, Nara H, Cho N, Naito M. Development of protein degradation inducers of oncogenic BCR-ABL protein by conjugation of ABL kinase inhibitors and IAP ligands. Cancer Sci 2017; 108:1657-1666. [PMID: 28556300 PMCID: PMC5543464 DOI: 10.1111/cas.13284] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 05/16/2017] [Accepted: 05/19/2017] [Indexed: 12/28/2022] Open
Abstract
Chromosomal translocation occurs in some cancer cells, which results in the expression of aberrant oncogenic fusion proteins that include BCR‐ABL in chronic myelogenous leukemia (CML). Inhibitors of ABL tyrosine kinase, such as imatinib and dasatinib, exhibit remarkable therapeutic effects, although emergence of drug resistance hampers the therapy during long‐term treatment. An alternative approach to treat CML is to downregulate the BCR‐ABL protein. We have devised a protein knockdown system by hybrid molecules named Specific and Non‐genetic inhibitor of apoptosis protein [IAP]‐dependent Protein Erasers (SNIPER), which is designed to induce IAP‐mediated ubiquitylation and proteasomal degradation of target proteins, and a couple of SNIPER(ABL) against BCR‐ABL protein have been developed recently. In this study, we tested various combinations of ABL inhibitors and IAP ligands, and the linker was optimized for protein knockdown activity of SNIPER(ABL). The resulting SNIPER(ABL)‐39, in which dasatinib is conjugated to an IAP ligand LCL161 derivative by polyethylene glycol (PEG) × 3 linker, shows a potent activity to degrade the BCR‐ABL protein. Mechanistic analysis suggested that both cellular inhibitor of apoptosis protein 1 (cIAP1) and X‐linked inhibitor of apoptosis protein (XIAP) play a role in the degradation of BCR‐ABL protein. Consistent with the degradation of BCR‐ABL protein, the SNIPER(ABL)‐39 inhibited the phosphorylation of signal transducer and activator of transcription 5 (STAT5) and Crk like proto‐oncogene (CrkL), and suppressed the growth of BCR‐ABL‐positive CML cells. These results suggest that SNIPER(ABL)‐39 could be a candidate for a degradation‐based novel anti‐cancer drug against BCR‐ABL‐positive CML.
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Affiliation(s)
- Norihito Shibata
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Tokyo, Japan
| | - Naoki Miyamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical, Kanagawa, Japan
| | - Katsunori Nagai
- Pharmaceutical Research Division, Takeda Pharmaceutical, Kanagawa, Japan
| | | | - Tomoya Sameshima
- Pharmaceutical Research Division, Takeda Pharmaceutical, Kanagawa, Japan
| | - Nobumichi Ohoka
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Tokyo, Japan
| | - Takayuki Hattori
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Tokyo, Japan
| | - Yasuhiro Imaeda
- Pharmaceutical Research Division, Takeda Pharmaceutical, Kanagawa, Japan
| | - Hiroshi Nara
- Pharmaceutical Research Division, Takeda Pharmaceutical, Kanagawa, Japan
| | - Nobuo Cho
- Pharmaceutical Research Division, Takeda Pharmaceutical, Kanagawa, Japan
| | - Mikihiko Naito
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Tokyo, Japan
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25
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Targeted protein knockdown using small molecule degraders. Curr Opin Chem Biol 2017; 39:46-53. [PMID: 28605671 DOI: 10.1016/j.cbpa.2017.05.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/29/2017] [Indexed: 02/07/2023]
Abstract
Small molecule probes of biological systems have traditionally been designed to bind to and inhibit the active sites of their protein targets. While this class of pharmacological agents has been broadened by the development of a small number of allosteric and protein-protein interaction (PPI) inhibitors, conventional drug design still excludes 'undruggable' proteins that are neither enzymes nor receptors. Recent years have seen the emergence of new classes of small molecules that can target hitherto undruggable proteins by recruiting the cellular proteostasis machinery to selectively tag them for degradation. These molecules, especially the class known as Proteolysis Targeting Chimera (PROTACs), represent a paradigm shift in chemical genetics, but their most tantalizing potential is as novel therapeutic agents. This review briefly summarizes the preclinical development of small molecule-based protein degraders, and describes the recent improvements in the technology that have positioned PROTACs on the cusp of entering the clinic.
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Okitsu K, Hattori T, Misawa T, Shoda T, Kurihara M, Naito M, Demizu Y. Development of a Small Hybrid Molecule That Mediates Degradation of His-Tag Fused Proteins. J Med Chem 2017; 61:576-582. [DOI: 10.1021/acs.jmedchem.7b00413] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Koyo Okitsu
- Division
of Organic Chemistry, National Institute of Health Sciences, 1-18-1,
Kamiyoga, Setagaya, Tokyo 158-8501, Japan
- Graduate
School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Takayuki Hattori
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya, Tokyo 158-8501, Japan
| | - Takashi Misawa
- Division
of Organic Chemistry, National Institute of Health Sciences, 1-18-1,
Kamiyoga, Setagaya, Tokyo 158-8501, Japan
| | - Takuji Shoda
- Division
of Organic Chemistry, National Institute of Health Sciences, 1-18-1,
Kamiyoga, Setagaya, Tokyo 158-8501, Japan
| | - Masaaki Kurihara
- Division
of Organic Chemistry, National Institute of Health Sciences, 1-18-1,
Kamiyoga, Setagaya, Tokyo 158-8501, Japan
| | - Mikihiko Naito
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya, Tokyo 158-8501, Japan
| | - Yosuke Demizu
- Division
of Organic Chemistry, National Institute of Health Sciences, 1-18-1,
Kamiyoga, Setagaya, Tokyo 158-8501, Japan
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Ottis P, Crews CM. Proteolysis-Targeting Chimeras: Induced Protein Degradation as a Therapeutic Strategy. ACS Chem Biol 2017; 12:892-898. [PMID: 28263557 DOI: 10.1021/acschembio.6b01068] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Until recently, the only ways to reduce specific protein signaling were to either knock down the target by RNAi or to interfere with the signaling by inhibiting an enzyme or receptor within the signal transduction cascade. Herein, we review an emerging class of small molecule pharmacological agents, called PROTACs, that present a novel approach to specifically target proteins and their respective signaling pathways. These heterobifunctional molecules utilize endogenous cellular quality control machinery by recruiting it to target proteins in order to induce their degradation.
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Affiliation(s)
- Philipp Ottis
- Department
of Molecular, Cellular and Developmental Biology, ‡Department of Chemistry, and §Department of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Department
of Molecular, Cellular and Developmental Biology, ‡Department of Chemistry, and §Department of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
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Collins I, Wang H, Caldwell JJ, Chopra R. Chemical approaches to targeted protein degradation through modulation of the ubiquitin-proteasome pathway. Biochem J 2017; 474:1127-1147. [PMID: 28298557 PMCID: PMC5350610 DOI: 10.1042/bcj20160762] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/04/2017] [Accepted: 01/16/2017] [Indexed: 12/11/2022]
Abstract
Manipulation of the ubiquitin-proteasome system to achieve targeted degradation of proteins within cells using chemical tools and drugs has the potential to transform pharmacological and therapeutic approaches in cancer and other diseases. An increased understanding of the molecular mechanism of thalidomide and its analogues following their clinical use has unlocked small-molecule modulation of the substrate specificity of the E3 ligase cereblon (CRBN), which in turn has resulted in the advancement of new immunomodulatory drugs (IMiDs) into the clinic. The degradation of multiple context-specific proteins by these pleiotropic small molecules provides a means to uncover new cell biology and to generate future drug molecules against currently undruggable targets. In parallel, the development of larger bifunctional molecules that bring together highly specific protein targets in complexes with CRBN, von Hippel-Lindau, or other E3 ligases to promote ubiquitin-dependent degradation has progressed to generate selective chemical compounds with potent effects in cells and in vivo models, providing valuable tools for biological target validation and with future potential for therapeutic use. In this review, we survey recent breakthroughs achieved in these two complementary methods and the discovery of new modes of direct and indirect engagement of target proteins with the proteasome. We discuss the experimental characterisation that validates the use of molecules that promote protein degradation as chemical tools, the preclinical and clinical examples disclosed to date, and the future prospects for this exciting area of chemical biology.
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Affiliation(s)
- Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, U.K
| | - Hannah Wang
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, U.K
| | - John J Caldwell
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, U.K
| | - Raj Chopra
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, U.K.
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Development of BCR-ABL degradation inducers via the conjugation of an imatinib derivative and a cIAP1 ligand. Bioorg Med Chem Lett 2016; 26:4865-4869. [DOI: 10.1016/j.bmcl.2016.09.041] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/12/2016] [Accepted: 09/15/2016] [Indexed: 11/20/2022]
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Toure M, Crews CM. Niedermolekulare PROTACs: neue Wege zum Abbau von Proteinen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201507978] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Momar Toure
- Departments of Chemistry; Molecular, Cellular & Developmental Biology; Pharmacology; Yale University; New Haven CT 06511 USA
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental Biology; Pharmacology; Yale University; New Haven CT 06511 USA
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32
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Toure M, Crews CM. Small-Molecule PROTACS: New Approaches to Protein Degradation. Angew Chem Int Ed Engl 2016; 55:1966-73. [DOI: 10.1002/anie.201507978] [Citation(s) in RCA: 379] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Momar Toure
- Departments of Chemistry; Molecular, Cellular & Developmental Biology, Pharmacology; Yale University; New Haven CT 06511 USA
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental Biology, Pharmacology; Yale University; New Haven CT 06511 USA
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33
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Tinworth CP, Lithgow H, Churcher I. Small molecule-mediated protein knockdown as a new approach to drug discovery. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00347h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Research into degradation of cellular proteins induced by small molecule agents known as Protacs has gathered pace recently. This article reviews recent progress and assesses the challenges to be addressed to enable clinical evaluation of agents.
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Affiliation(s)
| | - Hannah Lithgow
- GlaxoSmithKline
- Medicines Research Centre
- Stevenage
- UK
- Department of Pure and Applied Chemistry
| | - Ian Churcher
- GlaxoSmithKline
- Medicines Research Centre
- Stevenage
- UK
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34
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Bondeson DP, Mares A, Smith IED, Ko E, Campos S, Miah AH, Mulholland KE, Routly N, Buckley DL, Gustafson JL, Zinn N, Grandi P, Shimamura S, Bergamini G, Faelth-Savitski M, Bantscheff M, Cox C, Gordon DA, Willard RR, Flanagan JJ, Casillas LN, Votta BJ, den Besten W, Famm K, Kruidenier L, Carter PS, Harling JD, Churcher I, Crews CM. Catalytic in vivo protein knockdown by small-molecule PROTACs. Nat Chem Biol 2015; 11:611-7. [PMID: 26075522 PMCID: PMC4629852 DOI: 10.1038/nchembio.1858] [Citation(s) in RCA: 804] [Impact Index Per Article: 89.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/03/2015] [Indexed: 01/01/2023]
Abstract
The current predominant therapeutic paradigm is based on maximizing drug-receptor occupancy to achieve clinical benefit. This strategy, however, generally requires excessive drug concentrations to ensure sufficient occupancy, often leading to adverse side effects. Here, we describe major improvements to the proteolysis targeting chimeras (PROTACs) method, a chemical knockdown strategy in which a heterobifunctional molecule recruits a specific protein target to an E3 ubiquitin ligase, resulting in the target's ubiquitination and degradation. These compounds behave catalytically in their ability to induce the ubiquitination of super-stoichiometric quantities of proteins, providing efficacy that is not limited by equilibrium occupancy. We present two PROTACs that are capable of specifically reducing protein levels by >90% at nanomolar concentrations. In addition, mouse studies indicate that they provide broad tissue distribution and knockdown of the targeted protein in tumor xenografts. Together, these data demonstrate a protein knockdown system combining many of the favorable properties of small-molecule agents with the potent protein knockdown of RNAi and CRISPR.
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Affiliation(s)
- Daniel P Bondeson
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Alina Mares
- GSK Medicines Research Centre, Stevenage, UK
| | | | - Eunhwa Ko
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | | | | | | | | | - Dennis L Buckley
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Jeffrey L Gustafson
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Nico Zinn
- Cellzome, a GSK company, Heidelberg, Germany
| | | | | | | | | | | | - Carly Cox
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | | | | | | | - Linda N Casillas
- Pattern Recognition Receptor Discovery Performance Unit, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Bartholomew J Votta
- Pattern Recognition Receptor Discovery Performance Unit, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Willem den Besten
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | | | | | | | | | | | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Department of Pharmacology, Yale University, New Haven, Connecticut, USA
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35
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Buckley DL, Crews CM. Small-molecule control of intracellular protein levels through modulation of the ubiquitin proteasome system. Angew Chem Int Ed Engl 2014; 53:2312-30. [PMID: 24459094 PMCID: PMC4348030 DOI: 10.1002/anie.201307761] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Indexed: 12/25/2022]
Abstract
Traditionally, biological probes and drugs have targeted the activities of proteins (such as enzymes and receptors) that can be readily controlled by small molecules. The remaining majority of the proteome has been deemed "undruggable". By using small-molecule modulators of the ubiquitin proteasome, protein levels, rather than protein activity, can be targeted instead, thus increasing the number of druggable targets. Whereas targeting of the proteasome itself can lead to a global increase in protein levels, the targeting of other components of the UPS (e.g., the E3 ubiquitin ligases) can lead to an increase in protein levels in a more targeted fashion. Alternatively, multiple strategies for inducing protein degradation with small-molecule probes are emerging. With the ability to induce and inhibit the degradation of targeted proteins, small-molecule modulators of the UPS have the potential to significantly expand the druggable portion of the proteome beyond traditional targets, such as enzymes and receptors.
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Affiliation(s)
- Dennis L. Buckley
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
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36
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Buckley DL, Crews CM. Steuerung der intrazellulären Proteinmenge durch niedermolekulare Modulatoren des Ubiquitin-Proteasom-Systems. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307761] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Swanson HI, Choi EY, Helton WB, Gairola CG, Valentino J. Impact of apigenin and kaempferol on human head and neck squamous cell carcinoma. Oral Surg Oral Med Oral Pathol Oral Radiol 2013; 117:214-20. [PMID: 24439916 DOI: 10.1016/j.oooo.2013.10.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/27/2013] [Accepted: 10/17/2013] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Apigenin and kaempferol are plant flavonoids with reported chemopreventive activities. This study aimed to determine the effect of apigenin and kaempferol on cell viability in cultured cells derived from the pharynx (FaDu cell line), an oral cavity carcinoma (PCI-13 cell line), and a metastatic lymph node (PCI-15B cell line) and in explanted FaDu cells. STUDY DESIGN The in vitro viability of FaDu, PCI-13, and PCI-15B cells treated with apigenin and kaempferol was determined. Tumor growth of FaDu explants was evaluated in athymic mice that were gavaged with either apigenin or kaempferol. RESULTS Although apigenin and kaempferol treatment decreased viability of cells in vitro, cell-type-dependent differences in responsiveness were observed. In vivo apigenin treatment significantly increased the tumor size of FaDu explants. Results obtained using kaempferol were similar. CONCLUSIONS The in vitro decrease in FaDu cell viability by apigenin and kaempferol was not observed in in vivo tumor explants using the conditions described in this study.
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Affiliation(s)
- Hollie I Swanson
- Professor, Department of Molecular and Biomedical Pharmacology, University of Kentucky College of Medicine, Lexington, KY, USA.
| | - Eun-Young Choi
- Professor, Department of Molecular and Biomedical Pharmacology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - W Brian Helton
- Partner, Mark Veronneau Plastics and ENT, Prestonsburg, KY, USA
| | - C Gary Gairola
- Professor, Graduate Center for Toxicology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Joseph Valentino
- Professor, Division of Otolaryngology-Head and Neck Surgery, University of Kentucky College of Medicine, Lexington, KY, USA
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38
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Abstract
In recent years, small interference RNAs (siRNAs) have greatly enhanced our understanding of protein functions by allowing knockdown of targeted proteins at the mRNA level. Similarly, in an effort to achieve degradation of targeted proteins at the post-translational level, chimeric small molecules called "PROTACs" (PROteolysis TArgeting Chimeric molecules) have been developed. The PROTAC approach utilizes chimeric small molecules which recruit targeted proteins to the ubiquitin-proteasome pathway, a major intracellular protein degradation system. Unlike conventional small molecules that bind to protein and inhibit its function, the PROTAC approach induces destruction of target protein via the ubiquitin-proteasome system. This article presents a typical strategy for PROTAC design and preparation and biological characterization. Curr. Protoc. Chem Biol. 2:71-87. © 2010 by John Wiley & Sons, Inc.
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Harmine and harmaline downregulate TCDD-induced Cyp1a1 in the livers and lungs of C57BL/6 mice. BIOMED RESEARCH INTERNATIONAL 2013; 2013:258095. [PMID: 23509697 PMCID: PMC3591235 DOI: 10.1155/2013/258095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 09/24/2012] [Accepted: 09/24/2012] [Indexed: 12/22/2022]
Abstract
We previously demonstrated that Peganum harmala L. extract and its main active constituents, harmine and harmaline inhibit the 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-mediated induction of the carcinogen-activating enzyme, Cyp1a1, in vitro. However, the effect of both alkaloids on Cyp1a1 in vivo has not been investigated. Therefore, the aim of this study is to examine the effect of harmine and harmaline on TCDD-mediated induction of Cyp1a1 in mice livers and lungs. C57BL/6 male mice were distributed into four groups (n = 6). First group received vehicle, while the second group received TCDD (i.p.). The third and fourth groups received either harmine or harmaline (i.p.) × 3 times along with TCDD one time with the mid dose of harmine and harmaline. All mice were sacrificed after 14 h from TCDD injection, and livers and lungs were isolated. The effect of harmine and harmaline on TCDD-mediated induction of Cyp1a1 mRNA, protein, and activity levels was determined using real-time PCR, Western blot analysis, and 7-ethoxyresurofin as a substrate, respectively. Our results showed that harmine and harmaline significantly decreased the TCDD-mediated induction of Cyp1a1 in both the livers and lungs. We concluded that harmine and harmaline are promising candidate to inhibit TCDD-mediated induction of Cyp1a1 in mice hepatic and extrahepatic tissues.
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Abstract
The combination of two different and independently acting compounds into one covalently linked hybrid compound can convey synergy from the effects of both independently acting moieties to the new composite compound, leading to a pharmacological potency greater than the sum of each individual moiety's potencies. Here, we review a variety of such hybrid compounds, which can consist of various functional parts, molecular recognition or subcellular targeting moieties, or combinations thereof, acting either simultaneously or sequentially. Such moieties within a hybrid compound can consist of a variety of substance classes, including small organic molecules, polypeptides or nucleic acids identified either via rational molecular design or selection from libraries. Precedent for hybrid compounds comes from naturally occurring proteins and small molecules, such as botulinum toxin and bleomycin, which are secreted by micro-organisms. We review the high degree of suitability of hybrid compounds for the treatment of multifactorial diseases by simultaneously hitting several targets along an identified disease pathway. Examples are hybrid compounds against Alzheimer's disease, against the cancer-relevant phosphoinisitide-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) and epidermal growth factor signaling cascade, or in antimalarial therapy via simultaneous hitting of different mechanisms of hemozoin formation. Molecular recognition by peptides or aptamers (recognition-specific RNA or peptide sequences) can be combined with the transport of small molecule β-sheet breakers or toxins, or targeting to ubiquitin-dependent proteolysis. The vision of molecular nanomachines is currently realized in sequentially acting modular nanotransporters, consisting of four modules including a target, a membrane and nuclear translocation sequence, as well as a drug attachment domain. Through the rational combination of existing drugs and the synergy of their effects, a rapid amplification of their potency may be achieved, greatly accelerating drug development. A further enhancement of simultaneous multitarget action is enabled through the design of multifunctional hybrid drugs with sequential effects that make these hybrid molecules resemble intelligent nanomachines.
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Mohebati A, Guttenplan JB, Kochhar A, Zhao ZL, Kosinska W, Subbaramaiah K, Dannenberg AJ. Carnosol, a constituent of Zyflamend, inhibits aryl hydrocarbon receptor-mediated activation of CYP1A1 and CYP1B1 transcription and mutagenesis. Cancer Prev Res (Phila) 2012; 5:593-602. [PMID: 22374940 PMCID: PMC3324618 DOI: 10.1158/1940-6207.capr-12-0002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The aryl hydrocarbon receptor (AhR), a ligand-activated member of the basic helix-loop-helix family of transcription factors, plays a significant role in polycyclic aromatic hydrocarbon (PAH)-induced carcinogenesis. In the upper aerodigestive tract of humans, tobacco smoke, a source of PAHs, activates the AhR leading to increased expression of CYP1A1 and CYP1B1, which encode proteins that convert PAHs to genotoxic metabolites. Inhibitors of Hsp90 ATPase cause a rapid decrease in levels of AhR, an Hsp90 client protein, and thereby block PAH-mediated induction of CYP1A1 and CYP1B1. The main objective of this study was to determine whether Zyflamend, a polyherbal preparation, suppressed PAH-mediated induction of CYP1A1 and CYP1B1 and inhibited DNA adduct formation and mutagenesis. We also investigated whether carnosol, one of multiple phenolic antioxidants in Zyflamend, had similar inhibitory effects. Treatment of cell lines derived from oral leukoplakia (MSK-Leuk1) and skin (HaCaT) with benzo[a]pyrene (B[a]P), a prototypic PAH, induced CYP1A1 and CYP1B1 transcription, resulting in enhanced levels of message and protein. Both Zyflamend and carnosol suppressed these effects of B[a]P. Notably, both Zyflamend and carnosol inhibited Hsp90 ATPase activity and caused a rapid reduction in AhR levels. The formation of B[a]P-induced DNA adducts and mutagenesis was also inhibited by Zyflamend and carnosol. Collectively, these results show that Zyflamend and carnosol inhibit Hsp90 ATPase leading to reduced levels of AhR, suppression of B[a]P-mediated induction of CYP1A1 and CYP1B1, and inhibition of mutagenesis. Carnosol-mediated inhibition of Hsp90 ATPase activity can help explain the chemopreventive activity of herbs such as Rosemary, which contain this phenolic antioxidant.
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Affiliation(s)
- Arash Mohebati
- Department of Surgery (Head and Neck Service), Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Joseph B. Guttenplan
- Department of Basic Sciences, College of Dentistry; Department of Environmental Medicine, School of Medicine, New York University, New York, New York
| | - Amit Kochhar
- Department of Medicine, Weill Medical College of Cornell University, New York, New York
- Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Zhong-Lin Zhao
- Department of Basic Sciences, College of Dentistry; Department of Environmental Medicine, School of Medicine, New York University, New York, New York
| | - Wieslawa Kosinska
- Department of Basic Sciences, College of Dentistry; Department of Environmental Medicine, School of Medicine, New York University, New York, New York
| | - Kotha Subbaramaiah
- Department of Medicine, Weill Medical College of Cornell University, New York, New York
| | - Andrew J. Dannenberg
- Department of Medicine, Weill Medical College of Cornell University, New York, New York
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42
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Abstract
Small-molecule modulators of protein activity are increasingly being utilized as tools to examine the functional roles of proteins. Operating at the post-translational level, these molecules provide enhanced temporal and spatial control and mitigate the potential for compensatory responses in comparison with classical genetic approaches. Proteolysis targeting chimeric molecules, or PROTACs, are small molecules that inhibit the function of their target proteins by targeting them for degradation by the ubiquitin proteasome system. This chapter summarizes strategies for PROTAC preparation and characterization.
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43
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El Gendy MAM, Soshilov AA, Denison MS, El-Kadi AOS. Harmaline and harmalol inhibit the carcinogen-activating enzyme CYP1A1 via transcriptional and posttranslational mechanisms. Food Chem Toxicol 2011; 50:353-62. [PMID: 22037238 DOI: 10.1016/j.fct.2011.10.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 09/03/2011] [Accepted: 10/14/2011] [Indexed: 01/28/2023]
Abstract
Dioxins are known to cause several human cancers through activation of the aryl hydrocarbon receptor (AhR). Harmaline and harmalol are dihydro-β-carboline compounds present in several medicinal plants such as Peganum harmala. We have previously demonstrated the ability of P. harmala extract to inhibit TCDD-mediated induction of Cyp1a1 in murine hepatoma Hepa 1c1c7 cells. Therefore, the aim of this study is to examine the effect of harmaline and its main metabolite, harmalol, on dioxin-mediated induction of CYP1A1 in human hepatoma HepG2 cells. Our results showed that harmaline and harmalol at concentrations of (0.5-12.5μM) significantly inhibited the dioxin-induced CYP1A1 at mRNA, protein and activity levels in a concentration-dependent manner. The role of AhR was determined by the inhibition of the TCDD-mediated induction of AhR-dependent luciferase activity and the AhR/ARNT/XRE formation by both harmaline and harmalol. In addition, harmaline significantly displaced [(3)H]TCDD in the competitive ligand binding assay. At posttranslational level, both harmaline and harmalol decreased the protein stability of CYP1A1, suggesting that posttranslational modifications are involved. Moreover, the posttranslational modifications of harmaline and harmalol involve ubiquitin-proteasomal pathway and direct inhibitory effects of both compounds on CYP1A1 enzyme. These data suggest that harmaline and harmalol are promising agents for preventing dioxin-mediated effects.
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Affiliation(s)
- Mohamed A M El Gendy
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2N8
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El Gendy MAM, Soshilov AA, Denison MS, El-Kadi AOS. Transcriptional and posttranslational inhibition of dioxin-mediated induction of CYP1A1 by harmine and harmol. Toxicol Lett 2011; 208:51-61. [PMID: 22001777 DOI: 10.1016/j.toxlet.2011.09.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/13/2011] [Accepted: 09/14/2011] [Indexed: 10/16/2022]
Abstract
Dioxins are widespread environmental contaminants that induce the carcinogen-activating enzyme, cytochrome P450 1A1 (CYP1A1) through an aryl hydrocarbon receptor (AhR)-dependent mechanism. We previously demonstrated that harmine inhibits the dioxin-mediated induction of Cyp1a1 activity in murine hepatoma cells. Therefore, the aim of this study is to determine the effect of harmine and its main metabolite, harmol, on the dioxin-mediated induction of CYP1A1 in human HepG2 and murine Hepa 1c1c7 hepatoma cells. Our results showed that harmine and harmol significantly inhibited the dioxin-mediated induction of CYP1A1 at mRNA, protein, and activity levels in a concentration-dependent manner in human and murine hepatoma cells. Moreover, harmine and harmol inhibited the AhR-dependent luciferase activity and the activation and transformation of AhR using the electrophoretic mobility shift assay. In addition, harmine and harmol displaced [(3)H]TCDD in the competitive ligand binding assay. At posttranslational level, both harmine and harmol decreased the protein stability of CYP1A1, suggesting that posttranslational mechanism is involved. Furthermore, we demonstrated that the underlying mechanisms of the posttranslational modifications of both compounds involve ubiquitin-proteasomal pathway and direct inhibitory effects of CYP1A1 enzyme. We concluded that harmine and its metabolite, harmol, are new inhibitors of dioxin-mediated effects.
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Affiliation(s)
- Mohamed A M El Gendy
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2N8
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Itoh Y, Kitaguchi R, Ishikawa M, Naito M, Hashimoto Y. Design, synthesis and biological evaluation of nuclear receptor-degradation inducers. Bioorg Med Chem 2011; 19:6768-78. [PMID: 22014751 DOI: 10.1016/j.bmc.2011.09.041] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 09/21/2011] [Accepted: 09/22/2011] [Indexed: 12/15/2022]
Abstract
Compounds that regulate the function(s) of nuclear receptors (NRs) are useful for biological studies and as candidate therapeutic agents. Most such compounds are agonists or antagonists. On the other hand, we have developed specific protein degradation inducers, which we designated as SNIPERs (Specific and Nongenetic IAPs-dependent Protein ERasers), for selective degradation of target proteins. SNIPERs are hybrid molecules consisting of an appropriate ligand for the protein of interest, coupled to a ligand for inhibitor of apoptosis proteins (IAPs), which target the bound protein for polyubiquitination and proteasomal degradation. We considered that protein knockdown with SNIPERs would be a promising alternative approach for modulating NR function. In this study, we designed and synthesized degradation inducers targeting retinoic acid receptor (RAR), estrogen receptor (ER), and androgen receptor (AR). These newly synthesized RAR, ER, and AR SNIPERs, 9, 11, and 13, respectively, were confirmed to significantly reduce the levels of the corresponding NRs in live cells.
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Affiliation(s)
- Yukihiro Itoh
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Itoh Y, Ishikawa M, Kitaguchi R, Sato S, Naito M, Hashimoto Y. Development of target protein-selective degradation inducer for protein knockdown. Bioorg Med Chem 2011; 19:3229-41. [PMID: 21515062 DOI: 10.1016/j.bmc.2011.03.057] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 03/22/2011] [Accepted: 03/24/2011] [Indexed: 11/25/2022]
Abstract
Our previous technique for inducing selective degradation of target proteins with ester-type SNIPER (Specific and Nongenetic Inhibitor-of-apoptosis-proteins (IAPs)-dependent Protein ERaser) degrades both the target proteins and IAPs. Here, we designed a small-molecular amide-type SNIPER to overcome this issue. As proof of concept, we synthesized and biologically evaluated an amide-type SNIPER which induces selective degradation of cellular retinoic acid binding protein II (CRABP-II), but not IAPs. Such small-molecular, amide-type SNIPERs that induce target protein-selective degradation without affecting IAPs should be effective tools to study the biological roles of target proteins in living cells.
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Affiliation(s)
- Yukihiro Itoh
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Bunkyo-ku, Japan
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Cyrus K, Wehenkel M, Choi EY, Han HJ, Lee H, Swanson H, Kim KB. Impact of linker length on the activity of PROTACs. MOLECULAR BIOSYSTEMS 2011; 7:359-64. [PMID: 20922213 PMCID: PMC3835402 DOI: 10.1039/c0mb00074d] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Conventional genetic approaches have provided a powerful tool in the study of proteins. However, these techniques often preclude selective manipulation of temporal and spatial protein functions, which is crucial for the investigation of dynamic cellular processes. To overcome these limitations, a small molecule-based novel technology termed "PROteolysis TArgeting ChimeraS (PROTACs)" has been developed, targeting proteins for degradation at the post-translational level. Despite the promising potential of PROTACs to serve as molecular probes of complex signaling pathways, their design has not been generalized for broad application. Here, we present the first generalized approach for PROTAC design by fine-tuning the distance between the two participating partner proteins, the E3 ubiquitin ligase and the target protein. As such, we took a chemical approach to create estrogen receptor (ER)-α targeting PROTACs with varying linker lengths and the loss of the ER in cultured cells was monitored via western blot and fluorometric analyses. We found a significant effect of chain length on PROTAC efficacy, and, in this case, the optimum distance between the E3 recognition motif and the ligand was a 16 atom chain length. The information gathered from this experiment may offer a generalizable PROTAC design strategy to further the expansion of the PROTAC toolbox, opening new possibilities for the broad application of the PROTAC strategy in the study of multiple signaling pathways.
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Affiliation(s)
- Kedra Cyrus
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA 40536-0596. Fax: 859 257 7564; Tel: 859 257 5301
| | - Marie Wehenkel
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA 40536-0596. Fax: 859 257 7564; Tel: 859 257 5301
| | - Eun-Young Choi
- Department of Molecular and Biomedical Pharmacology, University of Kentucky, Lexington, Kentucky, USA 40536-0298
| | - Hyeong-Jun Han
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA 40536-0596. Fax: 859 257 7564; Tel: 859 257 5301
| | - Hyosung Lee
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA 40536-0596. Fax: 859 257 7564; Tel: 859 257 5301
| | - Hollie Swanson
- Department of Molecular and Biomedical Pharmacology, University of Kentucky, Lexington, Kentucky, USA 40536-0298
| | - Kyung-Bo Kim
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA 40536-0596. Fax: 859 257 7564; Tel: 859 257 5301
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Crews CM. Targeting the undruggable proteome: the small molecules of my dreams. ACTA ACUST UNITED AC 2010; 17:551-5. [PMID: 20609404 DOI: 10.1016/j.chembiol.2010.05.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 05/10/2010] [Accepted: 05/11/2010] [Indexed: 01/19/2023]
Abstract
Biologically active small molecules have long proven useful in the exploration of cell biology. Although many early compounds were by-products of drug development efforts, recent increased small molecule screening efforts in academia have expanded the repertoire of biological processes investigated to include areas of biology that are not of immediate pharmaceutical interest. Many of these new bioassays score for small molecule-induced phenotypic changes at the cellular or even organismal level and thus have been described as "chemical genetic" screens. However, this analogy with traditional genetic screens is misleading; although each gene has roughly an equivalent chance of being mutated in a traditional genetic screen, the amount of "proteomic space" that a chemical genetics approach can reach using current small molecule libraries is considerably smaller. Thus, new chemical biology methodologies are needed to target the remaining "undruggable proteome" with small druglike molecules.
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Affiliation(s)
- Craig M Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA.
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Cyrus K, Wehenkel M, Choi EY, Swanson H, Kim KB. Two-headed PROTAC: an effective new tool for targeted protein degradation. Chembiochem 2010; 11:1531-4. [PMID: 20572252 PMCID: PMC3852688 DOI: 10.1002/cbic.201000222] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Indexed: 12/21/2022]
Affiliation(s)
- Kedra Cyrus
- Department of Pharmaceutical Sciences University of Kentucky 789 South Limestone, Lexington, KY 40536-0596, USA
| | - Marie Wehenkel
- Department of Pharmaceutical Sciences University of Kentucky 789 South Limestone, Lexington, KY 40536-0596, USA
| | - Eun-Young Choi
- Department of Molecular and Biomedical Pharmacology University of Kentucky 800 Rose Street, Lexington, KY 40536, USA
| | - Hollie Swanson
- Department of Molecular and Biomedical Pharmacology University of Kentucky 800 Rose Street, Lexington, KY 40536, USA
| | - Kyung-Bo Kim
- Department of Pharmaceutical Sciences University of Kentucky 789 South Limestone, Lexington, KY 40536-0596, USA
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50
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Abstract
Protein degradation is the cell's mechanism of eliminating misfolded or unwanted proteins. The pathway by which proteins are degraded occurs through the ubiquitin-proteasome system. Ubiquitin is a small 9-kD (kDa) protein that is attached to proteins. A minimum of four ubiquitins are required for proteins to be recognized by the degradation machinery, known as the 26S proteasome. Defects in ubiquitination have been identified in a number of diseases, including cancer, neurodegenerative diseases, and metabolic disorders. We sought to exploit the delicate balance between protein synthesis and degradation to treat cancer by designing a chimeric molecule, known as Protac (Proteolysis Targeting Chimeric molecule). Protacs are heterobifunctional nanomolecules that are approximately 10 nm in size and can recruit proteins that cause cancer to the ubiquitin-proteasome machinery for degradation. In this review, we discuss the development of this novel technology for the treatment of cancer.
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Affiliation(s)
- Kathleen M Sakamoto
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA.
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