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Li Q, Zhou L, Qin S, Huang Z, Li B, Liu R, Yang M, Nice EC, Zhu H, Huang C. Proteolysis-targeting chimeras in biotherapeutics: Current trends and future applications. Eur J Med Chem 2023; 257:115447. [PMID: 37229829 DOI: 10.1016/j.ejmech.2023.115447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The success of inhibitor-based therapeutics is largely constrained by the acquisition of therapeutic resistance, which is partially driven by the undruggable proteome. The emergence of proteolysis targeting chimera (PROTAC) technology, designed for degrading proteins involved in specific biological processes, might provide a novel framework for solving the above constraint. A heterobifunctional PROTAC molecule could structurally connect an E3 ubiquitin ligase ligand with a protein of interest (POI)-binding ligand by chemical linkers. Such technology would result in the degradation of the targeted protein via the ubiquitin-proteasome system (UPS), opening up a novel way of selectively inhibiting undruggable proteins. Herein, we will highlight the advantages of PROTAC technology and summarize the current understanding of the potential mechanisms involved in biotherapeutics, with a particular focus on its application and development where therapeutic benefits over classical small-molecule inhibitors have been achieved. Finally, we discuss how this technology can contribute to developing biotherapeutic drugs, such as antivirals against infectious diseases, for use in clinical practices.
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Affiliation(s)
- Qiong Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Li Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyuan Qin
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Zhao Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Bowen Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Ruolan Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Mei Yang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Huili Zhu
- Department of Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, PR China.
| | - Canhua Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China; School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
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Venkatesan J, Murugan D, Rangasamy L. A Perspective on Newly Emerging Proteolysis-Targeting Strategies in Antimicrobial Drug Discovery. Antibiotics (Basel) 2022; 11:1717. [PMID: 36551374 PMCID: PMC9774230 DOI: 10.3390/antibiotics11121717] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
Targeted protein degradation is a new aspect in the field of drug discovery. Traditionally, developing an antibiotic includes tedious and expensive processes, such as drug screening, lead optimization, and formulation. Proteolysis-targeting chimeras (PROTACs) are new-generation drugs that use the proteolytic mechanism to selectively degrade and eliminate proteins involved in human diseases. The application of PROTACs is explored immensely in the field of cancer, and various PROTACs are in clinical trials. Thus, researchers have a profound interest in pursuing PROTAC technology as a new weapon to fight pathogenic viruses and bacteria. This review highlights the importance of antimicrobial PROTACs and other similar "PROTAC-like" techniques to degrade pathogenic target proteins (i.e., viral/bacterial proteins). These techniques can perform specific protein degradation of the pathogenic protein to avoid resistance caused by mutations or abnormal expression of the pathogenic protein. PROTAC-based antimicrobial therapeutics have the advantage of high specificity and the ability to degrade "undruggable" proteins, such as nonenzymatic and structural proteins.
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Affiliation(s)
- Janarthanan Venkatesan
- Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular, and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- School of Advanced Sciences (SAS), Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Dhanashree Murugan
- Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular, and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Loganathan Rangasamy
- Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular, and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
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Domostegui A, Nieto-Barrado L, Perez-Lopez C, Mayor-Ruiz C. Chasing molecular glue degraders: screening approaches. Chem Soc Rev 2022; 51:5498-5517. [PMID: 35723413 DOI: 10.1039/d2cs00197g] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein-protein interactions (PPIs) govern all biological processes. Some small molecules modulate PPIs through induced protein proximity. In particular, molecular glue degraders are monovalent compounds that orchestrate interactions between a target protein and an E3 ubiquitin ligase, prompting the proteasomal degradation of the former. This and other pharmacological strategies of targeted protein degradation (e.g. proteolysis-targeting chimeras - PROTACs) overcome some limitations of traditional occupancy-based therapeutics. Here, we provide an overview of the "molecular glue" concept, with a special focus on natural and synthetic inducers of proximity to E3s. We then briefly highlight the serendipitous discoveries of some clinical and preclinical molecular glue degraders, and discuss the first examples of intentional discoveries. Specifically, we outline the different screening strategies reported in this rapidly evolving arena and our thoughts on future perspectives. By mastering the ability to influence PPIs, molecular glue degraders can induce the degradation of unligandable proteins, thus providing an exciting path forward to broaden the targetable proteome.
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Affiliation(s)
- Ana Domostegui
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Luis Nieto-Barrado
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Carles Perez-Lopez
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Cristina Mayor-Ruiz
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
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Barghout SH. Targeted Protein Degradation: An Emerging Therapeutic Strategy in Cancer. Anticancer Agents Med Chem 2021; 21:214-230. [PMID: 32275492 DOI: 10.2174/1871520620666200410082652] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/20/2020] [Accepted: 02/19/2020] [Indexed: 11/22/2022]
Abstract
Drug discovery in the scope of cancer therapy has been focused on conventional agents that nonselectively induce DNA damage or selectively inhibit the activity of key oncogenic molecules without affecting their protein levels. An emerging therapeutic strategy that garnered attention in recent years is the induction of Targeted Protein Degradation (TPD) of cellular targets by hijacking the intracellular proteolysis machinery. This novel approach offers several advantages over conventional inhibitors and introduces a paradigm shift in several pharmacological aspects of drug therapy. While TPD has been found to be the major mode of action of clinically approved anticancer agents such as fulvestrant and thalidomide, recent years have witnessed systematic endeavors to expand the repertoire of proteins amenable to therapeutic ablation by TPD. Such endeavors have led to three major classes of agents that induce protein degradation, including molecular glues, Proteolysis Targeting Chimeras (PROTACs) and Hydrophobic Tag (HyT)-based degraders. Here, we briefly highlight agents in these classes and key advances made in the field with a focus on clinical translation in cancer therapy.
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Affiliation(s)
- Samir H Barghout
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
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Abstract
Targeted protein degradation is a broad and expanding field aimed at the modulation of protein homeostasis. A focus of this field has been directed toward molecules that hijack the ubiquitin proteasome system with heterobifunctional ligands that recruit a target protein to an E3 ligase to facilitate polyubiquitination and subsequent degradation by the 26S proteasome. Despite the success of these chimeras toward a number of clinically relevant targets, the ultimate breadth and scope of this approach remains uncertain. Here we highlight recent advances in assays and tools available to evaluate targeted protein degradation, including and beyond the study of E3-targeted chimeric ligands. We note several challenges associated with degrader development and discuss various approaches to expanding the protein homeostasis toolbox.
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Jaeger MG, Winter GE. Fast-acting chemical tools to delineate causality in transcriptional control. Mol Cell 2021; 81:1617-1630. [PMID: 33689749 DOI: 10.1016/j.molcel.2021.02.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/20/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Abstract
Multi-dimensional omics profiling continues to illuminate the complexity of cellular processes. Because of difficult mechanistic interpretation of phenotypes induced by slow perturbation, fast experimental setups are increasingly used to dissect causal interactions directly in cells. Here we review a growing body of studies that leverage rapid pharmacological perturbation to delineate causality in gene control. When coupled with kinetically matched readouts, fast chemical genetic tools allow recording of primary phenotypes before confounding secondary effects manifest. The toolbox encompasses directly acting probes, such as active-site inhibitors and proteolysis-targeting chimeras, as well as strategies using genetic engineering to render target proteins chemically tractable, such as analog-sensitive and degron systems. We anticipate that extrapolation of these concepts to single-cell setups will further transform our mechanistic understanding of transcriptional control in the future. Importantly, the concept of leveraging speed to derive causality should be broadly applicable to many aspects of biological regulation.
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Affiliation(s)
- Martin G Jaeger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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Verma R. Exploiting Ubiquitin Ligases for Induced Target Degradation as an Antiviral Strategy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:339-357. [PMID: 34258747 DOI: 10.1007/978-981-16-0267-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Posttranslational modifications of targeted substrates alter their cellular fate. Ubiquitin is a highly conserved and ubiquitous covalent modifier protein that tags substrates with a single molecule or with a polyubiquitin chain. Monoubiquitination affects trafficking and signaling patterns of modified proteins. In contrast, polyubiquitination, particularly K48-linked polyubiquitination, targets the protein for degradation by the Ubiquitin-Proteasome System (UPS) resulting in a committed fate through irreversible inactivation of substrate. Given the diversity of cellular functions impacted by ubiquitination, it is no surprise that the wily pathogenic viruses have co-opted the UPS in myriad ways to ensure their survival. In this review, I describe viral exploitation of nondegradative ubiquitin signaling pathways to effect entry, replication, and egress. Additionally, viruses also harness the UPS to degrade antiviral cellular host factors. Finally, I describe how we can exploit the same proteolytic machinery to enable PROTACs (Proteolysis-Targeting Chimeras) to degrade essential viral proteins. Successful implementation of this modality will add to the arsenal of emerging antiviral therapies.
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Affiliation(s)
- Rati Verma
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, CA, USA.
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8
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The promise and current status of CDK12/13 inhibition for the treatment of cancer. Future Med Chem 2020; 13:117-141. [PMID: 33295810 DOI: 10.4155/fmc-2020-0240] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
CDK12 and CDK13 are Ser/Thr protein kinases that regulate transcription and co-transcriptional processes. Genetic silencing of CDK12 is associated with genomic instability in a variety of cancers, including difficult-to-treat breast, ovarian, colorectal, brain and pancreatic cancers, and is synthetic lethal with PARP, MYC or EWS/FLI inhibition. CDK13 is amplified in hepatocellular carcinoma. Consequently, selective CDK12/13 inhibitors constitute powerful research tools as well as promising anti-cancer therapeutics, either alone or in combination therapy. Herein the authors discuss the role of CDK12 and CDK13 in normal and cancer cells, describe their utility as a biomarker and therapeutic target, review the medicinal chemistry optimization of existing CDK12/13 inhibitors and outline strategies for the rational design of CDK12/13 selective inhibitors.
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Prozzillo Y, Fattorini G, Santopietro MV, Suglia L, Ruggiero A, Ferreri D, Messina G. Targeted Protein Degradation Tools: Overview and Future Perspectives. BIOLOGY 2020; 9:biology9120421. [PMID: 33256092 PMCID: PMC7761331 DOI: 10.3390/biology9120421] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/28/2022]
Abstract
Simple Summary Gene inactivation is a powerful strategy to study the function of specific proteins in the context of cellular physiology that can be applied for only non-essential genes since their DNA sequence is destroyed. On the other hand, perturbing the amount of the transcript can lead to incomplete protein depletion and generate potential off-target effects. Instead, targeting at the protein level is desirable to overcome these limitations. In the last decade, several approaches have been developed and wisely improved, including compartment delocalization tools and protein degradation systems. This review highlights the most recent advances in targeted protein inactivation (TPI) and focuses on a putative novel tool to specifically degrade endogenous genetically unmodified target protein. Abstract Targeted protein inactivation (TPI) is an elegant approach to investigate protein function and its role in the cellular landscape, overcoming limitations of genetic perturbation strategies. These systems act in a reversible manner and reduce off-target effects exceeding the limitations of CRISPR/Cas9 and RNA interference, respectively. Several TPI have been developed and wisely improved, including compartment delocalization tools and protein degradation systems. However, unlike chemical tools such as PROTACs (PROteolysis TArgeting Chimeras), which work in a wild-type genomic background, TPI technologies require adding an aminoacidic signal sequence (tag) to the protein of interest (POI). On the other hand, the design and optimization of PROTACs are very laborious and time-consuming. In this review, we focus on anchor-away, deGradFP, auxin-inducible degron (AID) and dTAG technologies and discuss their recent applications and advances. Finally, we propose nano-grad, a novel nanobody-based protein degradation tool, which specifically proteolyzes endogenous tag-free target protein.
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Affiliation(s)
- Yuri Prozzillo
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (M.V.S.); (L.S.); (D.F.)
- Correspondence: (Y.P.); (G.M.)
| | - Gaia Fattorini
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (M.V.S.); (L.S.); (D.F.)
| | - Maria Virginia Santopietro
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (M.V.S.); (L.S.); (D.F.)
| | - Luigi Suglia
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (M.V.S.); (L.S.); (D.F.)
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 3BX, UK;
- Immune and Infectious Disease Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Diego Ferreri
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (M.V.S.); (L.S.); (D.F.)
| | - Giovanni Messina
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (M.V.S.); (L.S.); (D.F.)
- Pasteur Institute of Italy, Fondazione Cenci-Bolognetti, 00161 Rome, Italy
- Correspondence: (Y.P.); (G.M.)
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10
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Voutsadakis IA. Further Understanding of High-Grade Serous Ovarian Carcinogenesis: Potential Therapeutic Targets. Cancer Manag Res 2020; 12:10423-10437. [PMID: 33116896 PMCID: PMC7585777 DOI: 10.2147/cmar.s249540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/25/2020] [Indexed: 01/09/2023] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) is the most common type of ovarian cancer and the most lethal gynecologic malignancy due to advanced stage at presentation. Recent years have witnessed progress in the therapy of HGSOC with the introduction of PARP (poly-adenosine diphosphate ribose polymerase) inhibitors and the anti-angiogenic monoclonal antibody bevacizumab to the backbone of chemotherapy or as maintenance therapy after chemotherapy. The improved molecular understanding of ovarian cancer pathogenesis, which has brought these therapies into the clinic, aspires to extend the boundaries of therapies through elucidation of other molecular aspects of ovarian carcinogenesis. This accumulating knowledge has started to be translated to additional targeted therapies that are in various stages of development. These include inhibitors of the function of other proteins involved in homologous recombination deficiency (HRD), such as WEE1 kinase, ATM/ATR kinases and CDK12 inhibitors. Despite disappointing results with immune checkpoint inhibitors monotherapy, harnessing the immune system in HGSOC with combination therapies that promote antigen production and immune cell activation is an avenue being explored. This paper examines arising HGSOC therapies based on molecular understanding of pathogenesis.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste. Marie, Ontario, Canada
- Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, Ontario, Canada
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Abstract
In this issue of Cell Chemical Biology, Li et al. (2020), Hsu et al. (2020), and Potjewyd et al. (2020) expand the target spectrum amenable to protein degradation by designing degraders of the cell cycle checkpoint kinase Wee1 and the polycomb repressive complex 2 (PRC2) via its regulatory EED subunit.
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Affiliation(s)
- Martin G Jaeger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090 Vienna, Austria.
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12
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Bensimon A, Pizzagalli MD, Kartnig F, Dvorak V, Essletzbichler P, Winter GE, Superti-Furga G. Targeted Degradation of SLC Transporters Reveals Amenability of Multi-Pass Transmembrane Proteins to Ligand-Induced Proteolysis. Cell Chem Biol 2020; 27:728-739.e9. [PMID: 32386596 PMCID: PMC7303955 DOI: 10.1016/j.chembiol.2020.04.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/21/2020] [Accepted: 04/03/2020] [Indexed: 01/05/2023]
Abstract
With more than 450 members, the solute carrier (SLC) group of proteins represents the largest class of transporters encoded in the human genome. Their several-pass transmembrane domain structure and hydrophobicity contribute to the orphan status of many SLCs, devoid of known cargos or chemical inhibitors. We report that SLC proteins belonging to different families and subcellular compartments are amenable to induced degradation by heterobifunctional ligands. Engineering endogenous alleles via the degradation tag (dTAG) technology enabled chemical control of abundance of the transporter protein, SLC38A2. Moreover, we report the design of d9A-2, a chimeric compound engaging several members of the SLC9 family and leading to their degradation. d9A-2 impairs cellular pH homeostasis and promotes cell death in a range of cancer cell lines. These findings open the era of SLC-targeting chimeric degraders and demonstrate potential access of multi-pass transmembrane proteins of different subcellular localizations to the chemically exploitable degradation machinery.
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Affiliation(s)
- Ariel Bensimon
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Mattia D Pizzagalli
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Felix Kartnig
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Patrick Essletzbichler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria.
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Hanzl A, Winter GE. Targeted protein degradation: current and future challenges. Curr Opin Chem Biol 2020; 56:35-41. [PMID: 31901786 PMCID: PMC7615046 DOI: 10.1016/j.cbpa.2019.11.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/21/2022]
Abstract
Traditional approaches in the development of small-molecule drugs typically aim to inhibit the biochemical activity of functional protein domains. In contrast, targeted protein degradation aims to reduce overall levels of disease-relevant proteins. Mechanistically, this can be achieved via chemical ligands that induce molecular proximity between an E3 ubiquitin ligase and a protein of interest, leading to ubiquitination and degradation of the protein of interest. This paradigm-shifting pharmacology promises to address several limitations inherent to conventional inhibitor design. Most notably, targeted protein degradation has the potential not only to expand the druggable proteome beyond the reach of traditional competitive inhibitors but also to develop therapeutic strategies of unmatched selectivity. This review briefly summarizes key challenges that remain to be addressed to deliver on these promises and to realize the full therapeutic potential of pharmacologic modulation of protein degradation pathways.
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Affiliation(s)
- Alexander Hanzl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
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14
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Moreau K, Coen M, Zhang AX, Pachl F, Castaldi MP, Dahl G, Boyd H, Scott C, Newham P. Proteolysis-targeting chimeras in drug development: A safety perspective. Br J Pharmacol 2020; 177:1709-1718. [PMID: 32022252 DOI: 10.1111/bph.15014] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 12/11/2022] Open
Abstract
Proteolysis-targeting chimeras are a new drug modality that exploits the endogenous ubiquitin proteasome system to degrade a protein of interest for therapeutic benefit. As the first-generation of proteolysis-targeting chimeras have now entered clinical trials for oncology indications, it is timely to consider the theoretical safety risks inherent with this modality which include off-target degradation, intracellular accumulation of natural substrates for the E3 ligases used in the ubiquitin proteasome system, proteasome saturation by ubiquitinated proteins, and liabilities associated with the "hook effect" of proteolysis-targeting chimeras This review describes in vitro and non-clinical in vivo data that provide mechanistic insight of these safety risks and approaches being used to mitigate these risks in the next generation of proteolysis-targeting chimera molecules to extend therapeutic applications beyond life-threatening diseases.
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Affiliation(s)
- Kevin Moreau
- Oncology Safety, Clinical Pharmacology and Safety Sciences R&D, AstraZeneca, Cambridge, UK
| | - Muireann Coen
- Oncology Safety, Clinical Pharmacology and Safety Sciences R&D, AstraZeneca, Cambridge, UK
| | - Andrew X Zhang
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Boston, Massachusetts
| | - Fiona Pachl
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Boston, Massachusetts
| | - M Paola Castaldi
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Boston, Massachusetts
| | - Goran Dahl
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Helen Boyd
- Business Planning and Operations, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Clay Scott
- Oncology Safety, Clinical Pharmacology and Safety Sciences R&D, AstraZeneca, Boston, Massachusetts
| | - Pete Newham
- Oncology Safety, Clinical Pharmacology and Safety Sciences R&D, AstraZeneca, Cambridge, UK
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15
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Dalton SE, Campos S. Covalent Small Molecules as Enabling Platforms for Drug Discovery. Chembiochem 2020; 21:1080-1100. [DOI: 10.1002/cbic.201900674] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel E. Dalton
- Astex Pharmaceuticals 436 Cambridge Science Park Milton Road Cambridge CB4 0QA UK
| | - Sebastien Campos
- PharmaronDrug Discovery Services Europe Hertford Road Hoddesdon Hertfordshire EN11 9BU UK
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16
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Verma R, Mohl D, Deshaies RJ. Harnessing the Power of Proteolysis for Targeted Protein Inactivation. Mol Cell 2020; 77:446-460. [PMID: 32004468 DOI: 10.1016/j.molcel.2020.01.010] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/26/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022]
Abstract
Two decades into the twenty-first century, a confluence of breakthrough technologies wielded at the molecular level is presenting biologists with unique opportunities to unravel the complexities of the cellular world. CRISPR/Cas9 allows gene knock-outs, knock-ins, and single-base editing at chromosomal loci. RNA-based tools such as siRNA, antisense oligos, and morpholinos can be used to silence expression of specific genes. Meanwhile, protein knockdown tools that draw inspiration from natural regulatory mechanisms and facilitate elimination of native or degron-tagged proteins from cells are rapidly emerging. The acute and reversible reduction in protein levels enabled by these methods allows for precise determination of loss-of-function phenotypes free from secondary effects or compensatory adaptation that can confound nucleic-acid-based methods that involve slow depletion or permanent loss of a protein. In this Review, we summarize the ingenious ways biologists have exploited natural mechanisms for protein degradation to direct the elimination of specific proteins at will. This has led to advancements not only in basic research but also in the therapeutic space with the introduction of PROTACs into clinical trials for cancer patients.
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Affiliation(s)
- Rati Verma
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, CA 91320, USA.
| | - Dane Mohl
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
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Mus LM, Lambertz I, Claeys S, Kumps C, Van Loocke W, Van Neste C, Umapathy G, Vaapil M, Bartenhagen C, Laureys G, De Wever O, Bexell D, Fischer M, Hallberg B, Schulte J, De Wilde B, Durinck K, Denecker G, De Preter K, Speleman F. The ETS transcription factor ETV5 is a target of activated ALK in neuroblastoma contributing to increased tumour aggressiveness. Sci Rep 2020; 10:218. [PMID: 31937834 PMCID: PMC6959226 DOI: 10.1038/s41598-019-57076-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/05/2019] [Indexed: 02/08/2023] Open
Abstract
Neuroblastoma is an aggressive childhood cancer arising from sympatho-adrenergic neuronal progenitors. The low survival rates for high-risk disease point to an urgent need for novel targeted therapeutic approaches. Detailed molecular characterization of the neuroblastoma genomic landscape indicates that ALK-activating mutations are present in 10% of primary tumours. Together with other mutations causing RAS/MAPK pathway activation, ALK mutations are also enriched in relapsed cases and ALK activation was shown to accelerate MYCN-driven tumour formation through hitherto unknown ALK-driven target genes. To gain further insight into how ALK contributes to neuroblastoma aggressiveness, we searched for known oncogenes in our previously reported ALK-driven gene signature. We identified ETV5, a bona fide oncogene in prostate cancer, as robustly upregulated in neuroblastoma cells harbouring ALK mutations, and show high ETV5 levels downstream of the RAS/MAPK axis. Increased ETV5 expression significantly impacted migration, invasion and colony formation in vitro, and ETV5 knockdown reduced proliferation in a murine xenograft model. We also established a gene signature associated with ETV5 knockdown that correlates with poor patient survival. Taken together, our data highlight ETV5 as an intrinsic component of oncogenic ALK-driven signalling through the MAPK axis and propose that ETV5 upregulation in neuroblastoma may contribute to tumour aggressiveness.
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Affiliation(s)
- Liselot M Mus
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Irina Lambertz
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Shana Claeys
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Candy Kumps
- Department of Uro-gynaecology, Ghent University Hospital, Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Christophe Van Neste
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marica Vaapil
- Translational Cancer Research, Lund University, Lund, Sweden
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, 50937, Cologne, Germany.,Centre for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Genevieve Laureys
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Department of Paediatric Haematology and Oncology, Ghent University Hospital, Ghent, Belgium
| | - Olivier De Wever
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Laboratory of Experimental Cancer Research, Ghent University, Ghent, Belgium
| | - Daniel Bexell
- Translational Cancer Research, Lund University, Lund, Sweden
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, 50937, Cologne, Germany.,Centre for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johannes Schulte
- Department of Paediatric Oncology and Haematology, University Children's Hospital Essen, Essen, Germany.,Department of Paediatric Oncology and Haematology, Charité University Medical Centre Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Berlin, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Bram De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Paediatric Haematology and Oncology, Ghent University Hospital, Ghent, Belgium
| | - Kaat Durinck
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Geertrui Denecker
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Frank Speleman
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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Ciulli A, Farnaby W. Protein degradation for drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2019; 31:1-3. [PMID: 31200853 DOI: 10.1016/j.ddtec.2019.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Alessio Ciulli
- Professor of Chemical & Structural Biology, School of Life Sciences, University of Dundee, Division of Biological Chemistry and Drug Discovery, James Black Centre, Dow Street, Dundee DD1 5EH, United Kingdom
| | - William Farnaby
- Professor of Chemical & Structural Biology, School of Life Sciences, University of Dundee, Division of Biological Chemistry and Drug Discovery, James Black Centre, Dow Street, Dundee DD1 5EH, United Kingdom
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19
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Bishop TR, Zhang Y, Erb MA. Pharmacological Modulation of Transcriptional Coregulators in Cancer. Trends Pharmacol Sci 2019; 40:388-402. [PMID: 31078321 PMCID: PMC6746237 DOI: 10.1016/j.tips.2019.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 12/14/2022]
Abstract
Upon binding of transcription factors to cis-regulatory DNA sequences, transcriptional coregulators are required for the activation or suppression of chromatin-dependent transcriptional signaling. These coregulators are frequently implicated in oncogenesis via causal roles in dysregulated, malignant transcriptional control and represent one of the fastest-growing target classes in small-molecule drug discovery. However, challenges in targeting coregulators include identifying evidence of cancer-specific genetic dependency, matching the pharmacologically addressable protein fold to a functional role in disease pathology, and achieving the necessary selectivity to exploit a given genetic dependency. We discuss here how recent trends in cancer pharmacology have confronted these challenges, positioning coregulators as tractable targets in the development of new cancer therapies.
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Affiliation(s)
- Timothy R Bishop
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yuxiang Zhang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael A Erb
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Chan AKN, Chen CW. Rewiring the Epigenetic Networks in MLL-Rearranged Leukemias: Epigenetic Dysregulation and Pharmacological Interventions. Front Cell Dev Biol 2019; 7:81. [PMID: 31157223 PMCID: PMC6529847 DOI: 10.3389/fcell.2019.00081] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 04/30/2019] [Indexed: 12/26/2022] Open
Abstract
Leukemias driven by chromosomal translocation of the mixed-lineage leukemia gene (MLL or KMT2A) are highly prevalent in pediatric oncology. The poor survival rate and lack of an effective targeted therapy for patients with MLL-rearranged (MLL-r) leukemias emphasize an urgent need for improved knowledge and novel therapeutic approaches for these malignancies. The resulting chimeric products of MLL gene rearrangements, i.e., MLL-fusion proteins (MLL-FPs), are capable of transforming hematopoietic stem/progenitor cells (HSPCs) into leukemic blasts. The ability of MLL-FPs to reprogram HSPCs toward leukemia requires the involvement of multiple chromatin effectors, including the histone 3 lysine 79 methyltransferase DOT1L, the chromatin epigenetic reader BRD4, and the super elongation complex. These epigenetic regulators constitute a complicated network that dictates maintenance of the leukemia program, and therefore represent an important cluster of therapeutic opportunities. In this review, we will discuss the role of MLL and its fusion partners in normal HSPCs and hematopoiesis, including the links between chromatin effectors, epigenetic landscapes, and leukemia development, and summarize current approaches to therapeutic targeting of MLL-r leukemias.
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Affiliation(s)
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, United States
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