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Suranjika S, Barla P, Sharma N, Dey N. A review on ubiquitin ligases: Orchestrators of plant resilience in adversity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 347:112180. [PMID: 38964613 DOI: 10.1016/j.plantsci.2024.112180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/19/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Ubiquitin- proteasome system (UPS) is universally present in plants and animals, mediating many cellular processes needed for growth and development. Plants constantly defend themselves against endogenous and exogenous stimuli such as hormonal signaling, biotic stresses such as viruses, fungi, nematodes, and abiotic stresses like drought, heat, and salinity by developing complex regulatory mechanisms. Ubiquitination is a regulatory mechanism involving selective elimination and stabilization of regulatory proteins through the UPS system where E3 ligases play a central role; they can bind to the targets in a substrate-specific manner, followed by poly-ubiquitylation, and subsequent protein degradation by 26 S proteasome. Increasing evidence suggests different types of E3 ligases play important roles in plant development and stress adaptation. Herein, we summarize recent advances in understanding the regulatory roles of different E3 ligases and primarily focus on protein ubiquitination in plant-environment interactions. It also highlights the diversity and complexity of these metabolic pathways that enable plant to survive under challenging conditions. This reader-friendly review provides a comprehensive overview of E3 ligases and their substrates associated with abiotic and biotic stresses that could be utilized for future crop improvement.
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Affiliation(s)
- Sandhya Suranjika
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India; Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), KIIT Road, Patia, Bhubaneswar, Odisha, India
| | - Preeti Barla
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India
| | - Namisha Sharma
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India
| | - Nrisingha Dey
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India.
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2
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El-Mergawy R, Chafin L, Ovando-Ricardez JA, Rosas L, Tsai M, Rojas M, Mora AL, Mallampalli RK. FOXK2 targeting by the SCF-E3 ligase subunit FBXO24 for ubiquitin mediated degradation modulates mitochondrial respiration. J Biol Chem 2024; 300:107359. [PMID: 38735474 PMCID: PMC11209018 DOI: 10.1016/j.jbc.2024.107359] [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: 02/05/2024] [Revised: 04/05/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024] Open
Abstract
FOXK2 is a crucial transcription factor implicated in a wide array of biological activities and yet understanding of its molecular regulation at the level of protein turnover is limited. Here, we identify that FOXK2 undergoes degradation in lung epithelia in the presence of the virulent pathogens Pseudomonas aeruginosa and Klebsiella pneumoniae through ubiquitin-proteasomal processing. FOXK2 through its carboxyl terminus (aa 428-478) binds the Skp-Cullin-F-box ubiquitin E3 ligase subunit FBXO24 that mediates multisite polyubiquitylation of the transcription factor resulting in its nuclear degradation. FOXK2 was detected within the mitochondria and targeted depletion of the transcription factor or cellular expression of FOXK2 mutants devoid of key carboxy terminal domains significantly impaired mitochondrial function. In experimental bacterial pneumonia, Fbxo24 heterozygous mice exhibited preserved mitochondrial function and Foxk2 protein levels compared to WT littermates. The results suggest a new mode of regulatory control of mitochondrial energetics through modulation of FOXK2 cellular abundance.
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Affiliation(s)
- Rabab El-Mergawy
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Lexie Chafin
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Jose A Ovando-Ricardez
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Lorena Rosas
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - MuChun Tsai
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Mauricio Rojas
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Ana L Mora
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Rama K Mallampalli
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA.
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3
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Lu X, Chandravanshi M, Sabbasani VR, Gaikwad S, Hughitt VK, Gyabaah-Kessie N, Scroggins BT, Das S, Myint W, Clapp ME, Schwieters CD, Dyba MA, Bolhuis DL, Koscielniak JW, Andresson T, Emanuele MJ, Brown NG, Matsuo H, Chari R, Citrin DE, Mock BA, Swenson RE, Walters KJ. A structure-based designed small molecule depletes hRpn13 Pru and a select group of KEN box proteins. Nat Commun 2024; 15:2485. [PMID: 38509117 PMCID: PMC10954691 DOI: 10.1038/s41467-024-46644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
Proteasome subunit hRpn13 is partially proteolyzed in certain cancer cell types to generate hRpn13Pru by degradation of its UCHL5/Uch37-binding DEUBAD domain and retention of an intact proteasome- and ubiquitin-binding Pru domain. By using structure-guided virtual screening, we identify an hRpn13 binder (XL44) and solve its structure ligated to hRpn13 Pru by integrated X-ray crystallography and NMR to reveal its targeting mechanism. Surprisingly, hRpn13Pru is depleted in myeloma cells following treatment with XL44. TMT-MS experiments reveal a select group of off-targets, including PCNA clamp-associated factor PCLAF and ribonucleoside-diphosphate reductase subunit M2 (RRM2), that are similarly depleted by XL44 treatment. XL44 induces hRpn13-dependent apoptosis and also restricts cell viability by a PCLAF-dependent mechanism. A KEN box, but not ubiquitination, is required for XL44-induced depletion of PCLAF. Here, we show that XL44 induces ubiquitin-dependent loss of hRpn13Pru and ubiquitin-independent loss of select KEN box containing proteins.
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Affiliation(s)
- Xiuxiu Lu
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Monika Chandravanshi
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Venkata R Sabbasani
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Snehal Gaikwad
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - V Keith Hughitt
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nana Gyabaah-Kessie
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Bradley T Scroggins
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Wazo Myint
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michelle E Clapp
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Charles D Schwieters
- Computational Biomolecular Magnetic Resonance Core, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marzena A Dyba
- Biophysics Resource, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Janusz W Koscielniak
- Basic Science Program, Leidos Biomedical Research Inc., NMR Facility for Biological Research, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Michael J Emanuele
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hiroshi Matsuo
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Deborah E Citrin
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Beverly A Mock
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Rolf E Swenson
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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4
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Rizvi Z, Reddy GS, Gorde SM, Pundir P, Das D, Sijwali PS. Plasmodium falciparum contains functional SCF and CRL4 ubiquitin E3 ligases, and CRL4 is critical for cell division and membrane integrity. PLoS Pathog 2024; 20:e1012045. [PMID: 38416790 PMCID: PMC10927090 DOI: 10.1371/journal.ppat.1012045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 03/11/2024] [Accepted: 02/13/2024] [Indexed: 03/01/2024] Open
Abstract
Protein ubiquitination is essential for cellular homeostasis and regulation of several processes, including cell division and genome integrity. Ubiquitin E3 ligases determine substrate specificity for ubiquitination, and Cullin-RING E3 ubiquitin ligases (CRLs) make the largest group among the ubiquitin E3 ligases. Although conserved and most studied in model eukaryotes, CRLs remain underappreciated in Plasmodium and related parasites. To investigate the CRLs of human malaria parasite Plasmodium falciparum, we generated parasites expressing tagged P. falciparum cullin-1 (PfCullin-1), cullin-2 (PfCullin-2), Rbx1 (PfRbx1) and Skp1 (PfSkp1). PfCullin-1 and PfCullin-2 were predominantly expressed in erythrocytic trophozoite and schizont stages, with nucleocytoplasmic localization and chromatin association, suggesting their roles in different cellular compartments and DNA-associated processes. Immunoprecipitation, in vitro protein-protein interaction, and ubiquitination assay confirmed the presence of a functional Skp1-Cullin-1-Fbox (PfSCF) complex, comprising of PfCullin-1, PfRbx1, PfSkp1, PfFBXO1, and calcyclin binding protein. Immunoprecipitation, sequence analysis, and ubiquitination assay indicated that PfCullin-2 forms a functional human CRL4-like complex (PfCRL4), consisting of PfRbx1, cleavage and polyadenylation specificity factor subunit_A and WD40 repeat proteins. PfCullin-2 knock-down at the protein level, which would hinder PfCRL4 assembly, significantly decreased asexual and sexual erythrocytic stage development. The protein levels of several pathways, including protein translation and folding, lipid biosynthesis and transport, DNA replication, and protein degradation were significantly altered upon PfCullin-2 depletion, which likely reflects association of PfCRL4 with multiple pathways. PfCullin-2-depleted schizonts had poorly delimited merozoites and internal membraned structures, suggesting a role of PfCRL4 in maintaining membrane integrity. PfCullin-2-depleted parasites had a significantly lower number of nuclei/parasite than the normal parasites, indicating a crucial role of PfCRL4 in cell division. We demonstrate the presence of functional CRLs in P. falciparum, with crucial roles for PfCRL4 in cell division and maintaining membrane integrity.
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Affiliation(s)
- Zeba Rizvi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India
| | - G. Srinivas Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, UP, India
| | - Somesh M. Gorde
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, UP, India
| | - Priyanka Pundir
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India
| | - Divya Das
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India
| | - Puran Singh Sijwali
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, UP, India
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5
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Yang N, Kong B, Zhu Z, Huang F, Zhang L, Lu T, Chen Y, Zhang Y, Jiang Y. Recent advances in targeted protein degraders as potential therapeutic agents. Mol Divers 2024; 28:309-333. [PMID: 36790583 PMCID: PMC9930057 DOI: 10.1007/s11030-023-10606-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/12/2023] [Indexed: 02/16/2023]
Abstract
Targeted protein degradation (TPD) technology has gradually become widespread in the past 20 years, which greatly boosts the development of disease treatment. Contrary to small inhibitors that act on protein kinases, transcription factors, ion channels, and other targets they can bind to, targeted protein degraders could target "undruggable targets" and overcome drug resistance through ubiquitin-proteasome pathway (UPP) and lysosome pathway. Nowadays, some bivalent degraders such as proteolysis-targeting chimeras (PROTACs) have aroused great interest in drug discovery, and some of them have successfully advanced into clinical trials. In this review, to better understand the mechanism of degraders, we elucidate the targeted protein degraders according to their action process, relying on the ubiquitin-proteasome system or lysosome pathway. Then, we briefly summarize the study of PROTACs employing different E3 ligases. Subsequently, the effect of protein of interest (POI) ligands, linker, and E3 ligands on PROTAC degradation activity is also discussed in detail. Other novel technologies based on UPP and lysosome pathway have been discussed in this paper such as in-cell click-formed proteolysis-targeting chimeras (CLIPTACs), molecular glues, Antibody-PROTACs (Ab-PROTACs), autophagy-targeting chimeras, and lysosome-targeting chimeras. Based on the introduction of these degradation technologies, we can clearly understand the action process and degradation mechanism of these approaches. From this perspective, it will be convenient to obtain the development status of these drugs, choose appropriate degradation methods to achieve better disease treatment and provide basis for future research and simultaneously distinguish the direction of future research efforts.
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Affiliation(s)
- Na Yang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China
| | - Bo Kong
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China
| | - Zhaohong Zhu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China
| | - Fei Huang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China
| | - Liliang Zhang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China
| | - Tao Lu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, People's Republic of China
| | - Yadong Chen
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China.
| | - Yanmin Zhang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China.
| | - Yulei Jiang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, People's Republic of China.
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6
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Ramachandran S, Makukhin N, Haubrich K, Nagala M, Forrester B, Lynch DM, Casement R, Testa A, Bruno E, Gitto R, Ciulli A. Structure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2. Nat Commun 2023; 14:6345. [PMID: 37816714 PMCID: PMC10564737 DOI: 10.1038/s41467-023-41894-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 09/14/2023] [Indexed: 10/12/2023] Open
Abstract
The Src homology 2 (SH2) domain recognizes phosphotyrosine (pY) post translational modifications in partner proteins to trigger downstream signaling. Drug discovery efforts targeting the SH2 domains have long been stymied by the poor drug-like properties of phosphate and its mimetics. Here, we use structure-based design to target the SH2 domain of the E3 ligase suppressor of cytokine signaling 2 (SOCS2). Starting from the highly ligand-efficient pY amino acid, a fragment growing approach reveals covalent modification of Cys111 in a co-crystal structure, which we leverage to rationally design a cysteine-directed electrophilic covalent inhibitor MN551. We report the prodrug MN714 containing a pivaloyloxymethyl (POM) protecting group and evidence its cell permeability and capping group unmasking using cellular target engagement and in-cell 19F NMR spectroscopy. Covalent engagement at Cys111 competitively blocks recruitment of cellular SOCS2 protein to its native substrate. The qualified inhibitors of SOCS2 could find attractive applications as chemical probes to understand the biology of SOCS2 and its CRL5 complex, and as E3 ligase handles in proteolysis targeting chimera (PROTACs) to induce targeted protein degradation.
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Affiliation(s)
- Sarath Ramachandran
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Nikolai Makukhin
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
- Amphista Therapeutics Ltd, Cory Building, Granta Park, Great Abington, Cambridge, CB21 6GQ, United Kingdom
| | - Kevin Haubrich
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Manjula Nagala
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Beth Forrester
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Dylan M Lynch
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Ryan Casement
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Andrea Testa
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
- Amphista Therapeutics Ltd, Cory Building, Granta Park, Great Abington, Cambridge, CB21 6GQ, United Kingdom
| | - Elvira Bruno
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Rosaria Gitto
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Stagno D'Alcontres 31, Pole Papardo, 98166, Messina, Italy
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom.
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7
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Wurz RP, Rui H, Dellamaggiore K, Ghimire-Rijal S, Choi K, Smither K, Amegadzie A, Chen N, Li X, Banerjee A, Chen Q, Mohl D, Vaish A. Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation. Nat Commun 2023; 14:4177. [PMID: 37443112 PMCID: PMC10344917 DOI: 10.1038/s41467-023-39904-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Targeted protein degradation via "hijacking" of the ubiquitin-proteasome system using proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic modality. The design of PROTACs is challenging; multiple steps involved in PROTAC-induced degradation make it difficult to establish coherent structure-activity relationships. Herein, we characterize PROTAC-mediated ternary complex formation and degradation by employing von Hippel-Lindau protein (VHL) recruiting PROTACs for two different target proteins, SMARCA2 and BRD4. Ternary-complex attributes and degradation activity parameters are evaluated by varying components of the PROTAC's architecture. Ternary complex binding affinity and cooperativity correlates well with degradation potency and initial rates of degradation. Additionally, we develop a ternary-complex structure modeling workflow to calculate the total buried surface area at the interface, which is in agreement with the measured ternary complex binding affinity. Our findings establish a predictive framework to guide the design of potent degraders.
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Affiliation(s)
- Ryan P Wurz
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Huan Rui
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | | | | | - Kaylee Choi
- Amgen Research, Amgen Inc., South San Francisco, CA, USA
| | - Kate Smither
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | | | - Ning Chen
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Xiaofen Li
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | | | - Qing Chen
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Dane Mohl
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA.
| | - Amit Vaish
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA.
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8
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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: 3] [Impact Index Per Article: 3.0] [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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9
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Jin Y, Fan J, Wang R, Wang X, Li N, You Q, Jiang Z. Ligation to Scavenging Strategy Enables On-Demand Termination of Targeted Protein Degradation. J Am Chem Soc 2023; 145:7218-7229. [PMID: 36971523 DOI: 10.1021/jacs.2c12809] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Event-driven bifunctional molecules, typified by proteolysis targeting chimera (PROTAC) technology, have been successfully applied in degrading many proteins of interest (POI). Due to the unique catalytic mechanism, PROTACs will induce multiple cycles of degradation until the elimination of the target protein. Here, we propose a versatile "Ligation to scavenging" approach to terminate event-driven degradation for the first time. Ligation to the scavenging system consists of a TCO-modified dendrimer (PAMAM-G5-TCO) and tetrazine-modified PROTACs (Tz-PROTACs). PAMAM-G5-TCO can rapidly scavenge intracellular free PROTACs via an inverse electron demand Diels-Alder reaction and terminate the degradation of certain proteins in living cells. Thus, this work proposes a flexible chemical knockdown approach to adjust the levels of POI on-demand in living cells, which paves the way for controlled target protein degradation.
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10
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Chrestia JF, Turani O, Araujo NR, Hernando G, Esandi MDC, Bouzat C. Regulation of nicotinic acetylcholine receptors by post-translational modifications. Pharmacol Res 2023; 190:106712. [PMID: 36863428 DOI: 10.1016/j.phrs.2023.106712] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 03/04/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) comprise a family of pentameric ligand-gated ion channels widely distributed in the central and peripheric nervous system and in non-neuronal cells. nAChRs are involved in chemical synapses and are key actors in vital physiological processes throughout the animal kingdom. They mediate skeletal muscle contraction, autonomic responses, contribute to cognitive processes, and regulate behaviors. Dysregulation of nAChRs is associated with neurological, neurodegenerative, inflammatory and motor disorders. In spite of the great advances in the elucidation of nAChR structure and function, our knowledge about the impact of post-translational modifications (PTMs) on nAChR functional activity and cholinergic signaling has lagged behind. PTMs occur at different steps of protein life cycle, modulating in time and space protein folding, localization, function, and protein-protein interactions, and allow fine-tuned responses to changes in the environment. A large body of evidence demonstrates that PTMs regulate all levels of nAChR life cycle, with key roles in receptor expression, membrane stability and function. However, our knowledge is still limited, restricted to a few PTMs, and many important aspects remain largely unknown. There is thus a long way to go to decipher the association of aberrant PTMs with disorders of cholinergic signaling and to target PTM regulation for novel therapeutic interventions. In this review we provide a comprehensive overview of what is known about how different PTMs regulate nAChR.
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Affiliation(s)
- Juan Facundo Chrestia
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca 8000, Argentina
| | - Ornella Turani
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca 8000, Argentina
| | - Noelia Rodriguez Araujo
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca 8000, Argentina
| | - Guillermina Hernando
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca 8000, Argentina
| | - María Del Carmen Esandi
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca 8000, Argentina
| | - Cecilia Bouzat
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca 8000, Argentina.
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11
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Tunjic TM, Weber N, Brunsteiner M. Computer aided drug design in the development of proteolysis targeting chimeras. Comput Struct Biotechnol J 2023; 21:2058-2067. [PMID: 36968015 PMCID: PMC10030821 DOI: 10.1016/j.csbj.2023.02.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
Proteolysis targeting chimeras represent a class of drug molecules with a number of attractive properties, most notably a potential to work for targets that, so far, have been in-accessible for conventional small molecule inhibitors. Due to their different mechanism of action, and physico-chemical properties, many of the methods that have been designed and applied for computer aided design of traditional small molecule drugs are not applicable for proteolysis targeting chimeras. Here we review recent developments in this field focusing on three aspects: de-novo linker-design, estimation of absorption for beyond-rule-of-5 compounds, and the generation and ranking of ternary complex structures. In spite of this field still being young, we find that a good number of models and algorithms are available, with the potential to assist the design of such compounds in-silico, and accelerate applied pharmaceutical research.
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12
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Zhao L, Kang M, Liu X, Wang Z, Wang Y, Chen H, Liu W, Liu S, Li B, Li C, Chang A, Tang B. UBR7 inhibits HCC tumorigenesis by targeting Keap1/Nrf2/Bach1/HK2 and glycolysis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:330. [PMID: 36419136 PMCID: PMC9686014 DOI: 10.1186/s13046-022-02528-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/27/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Glycolysis metabolism is an attractive target for cancer therapy. Reprogramming metabolic pathways could improve the ability of metabolic inhibitors to suppress cancers with limited treatment options. The ubiquitin-proteasome system facilitates the turnover of most intracellular proteins with E3 ligase conferring the target selection and specificity. Ubiquitin protein ligase E3 component N-recognin 7 (UBR7), among the least studied E3 ligases, recognizes its substrate through a plant homeodomain (PHD) finger. Here, we bring into focus on its suppressive role in glycolysis and HCC tumorigenesis, dependent on its E3 ubiquitin ligase activity toward monoubiquitination of histone H2B at lysine 120 (H2BK120ub). METHODS In this study, we carried out high-throughput RNAi screening to identify epigenetic candidates in regulating lactic acid and investigated its possible roles in HCC progression. RESULTS UBR7 loss promotes HCC tumorigenesis both in vitro and in vivo. UBR7 inhibits glycolysis by indirectly suppressing HK2 expression, a downstream target of Nrf2/Bach1 axis. Mechanically, UBR7 regulates H2BK120ub to bind to Keap1 promoter through H2BK120ub monoubiquitination, thereby modulating Keap1 expression and downstream Nrf2/Bach1/HK2 signaling. Pharmaceutical and genetic inhibition of glycolytic enzymes attenuate the promoting effect of UBR7 deficiency on tumor growth. In addition, methyltransferase ALKBH5, downregulated in HCC, regulated UBR7 expression in an m6A-dependent manner. CONCLUSIONS These results collectively establish UBR7 as a critical negative regulator of aerobic glycolysis and HCC tumorigenesis through regulation of the Keap1/Nrf2/Bach1/HK2 axis, providing a potential clinical and therapeutic target for the HCC treatment.
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Affiliation(s)
- Liang Zhao
- grid.412594.f0000 0004 1757 2961Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, 530021 Guangxi People’s Republic of China
| | - Min Kang
- grid.412594.f0000 0004 1757 2961Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, 530021 Guangxi People’s Republic of China
| | - Xiaomeng Liu
- grid.412594.f0000 0004 1757 2961Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, 530021 Guangxi People’s Republic of China
| | - Zhenran Wang
- grid.412594.f0000 0004 1757 2961Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, 530021 Guangxi People’s Republic of China
| | - Yan Wang
- grid.412594.f0000 0004 1757 2961Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, 530021 Guangxi People’s Republic of China
| | - Haiqiang Chen
- grid.412594.f0000 0004 1757 2961Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, 530021 Guangxi People’s Republic of China
| | - Wenhui Liu
- grid.412594.f0000 0004 1757 2961Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, 530021 Guangxi People’s Republic of China
| | - Shiqian Liu
- grid.412594.f0000 0004 1757 2961Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, 530021 Guangxi People’s Republic of China
| | - Baibei Li
- grid.412594.f0000 0004 1757 2961Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, 530021 Guangxi People’s Republic of China
| | - Chong Li
- grid.9227.e0000000119573309Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Antao Chang
- grid.411918.40000 0004 1798 6427Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, 300060 China
| | - Bo Tang
- grid.412594.f0000 0004 1757 2961Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, 530021 Guangxi People’s Republic of China
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13
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Cao C, He M, Wang L, He Y, Rao Y. Chemistries of bifunctional PROTAC degraders. Chem Soc Rev 2022; 51:7066-7114. [PMID: 35916511 DOI: 10.1039/d2cs00220e] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteolysis targeting chimeras (PROTACs) technology is a novel and promising therapeutic strategy using small molecules to induce ubiquitin-dependent degradation of proteins. It has received extensive attention from both academia and industry as it can potentially access previously inaccessible targets. However, the design and optimization of PROTACs present big challenges for researchers, and the general strategy for its development and optimization is a lot of trial and error based on experience. This review highlights the important advances in this rapidly growing field and critical limitations of the traditional trial-and-error approach to developing PROTACs by analyzing numerous representative examples of PROTACs development. We summarize and analyze the general principles and strategies for PROTACs design and optimization from the perspective of chemical structure design, and propose potential future pathways to facilitate the development of PROTACs.
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Affiliation(s)
- Chaoguo Cao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China. .,Tsinghua-Peking Center for Life Sciences, Beijing 100084, P. R. China
| | - Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
| | - Liguo Wang
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
| | - Yuna He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
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14
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Lin Z, Woo CM. Methods to characterize and discover molecular degraders in cells. Chem Soc Rev 2022; 51:7115-7137. [PMID: 35899832 DOI: 10.1039/d2cs00261b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cells use many post-translational modifications (PTMs) to tailor proteins and transduce cellular signals. Recent years have witnessed the rapid growth of small molecule and enzymatic strategies to purposely manipulate one particular PTM, ubiquitination, on desired target proteins in cells. These approaches typically act by induced proximity between an E3 ligase and a target protein resulting in ubiquitination and degradation of the substrate in cells. In this review, we cover recent approaches to study molecular degraders and discover their induced substrates in vitro and in live cells. Methods that have been adapted and applied to the development of molecular degraders are described, including global proteomics, affinity-purification, chemical proteomics and enzymatic strategies. Extension of these strategies to edit additional PTMs in cells is also discussed. This review is intended to assist researchers who are interested in editing PTMs with new modalities to select suitable method(s) and guide their studies.
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Affiliation(s)
- Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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15
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Riching KM, Caine EA, Urh M, Daniels DL. The importance of cellular degradation kinetics for understanding mechanisms in targeted protein degradation. Chem Soc Rev 2022; 51:6210-6221. [PMID: 35792307 DOI: 10.1039/d2cs00339b] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeted protein degradation has exploded over the past several years due to preclinical and early clinical therapeutic success of numerous compounds, and the emergence of new degradation modalities, which has broadened the definition of what a degrader is. The most characterized and well-studied small molecule degraders are molecular glues and proteolysis targeting chimeras (PROTACs). These degraders induce a ternary complex between a target protein, degrader, and E3 ligase component, resulting in ubiquitination and subsequent degradation of the target protein via the ubiquitin proteasomal system (UPS). This event-driven process requires success at all steps through a complex cascade of events. As more systems, degraders, and targets are tested, it has become increasingly clear that achieving degradation is only the first critical milestone in a degrader development program. Rather highly efficacious degraders require a combination of multiple optimized parameters: rapid degradation, high potency, high maximal degradation (Dmax), and sustained loss of target without re-dosing. Success to meet these more rigorous goals depends upon the ability to characterize and understand the dynamic cellular degradation profiles and relate them to the underlying mechanism for any given target treated with a specific concentration of degrader. From this starting point, optimization and fine tuning of multiple kinetic parameters such as how fast degradation occurs (the rate), how much of the target is degraded (the extent), and how long the target remains degraded (the duration) can be performed. In this review we explore the diversity of cellular kinetic degradation profiles which can arise after molecular glue and PROTAC treatment and the potential implications of these varying responses. As the overall degradation kinetics are a sum of individual mechanistic steps, each with their own kinetic contributions, we discuss the ways in which changes at any one of these steps could potentially influence the resultant kinetic degradation profiles. Looking forward, we address the importance in characterizing the kinetics of target protein loss in the early stages of degrader design and how this will enable more rapid discovery of therapeutic agents to elicit desired phenotypic outcomes.
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Affiliation(s)
- Kristin M Riching
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Elizabeth A Caine
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Marjeta Urh
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Danette L Daniels
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
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16
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Webb T, Craigon C, Ciulli A. Targeting epigenetic modulators using PROTAC degraders: Current status and future perspective. Bioorg Med Chem Lett 2022; 63:128653. [PMID: 35257896 DOI: 10.1016/j.bmcl.2022.128653] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/10/2023]
Abstract
Epigenetic modulators perform critical functions in gene expression for rapid adaption to external stimuli and are prevalent in all higher-order organisms. The establishment of a link between dysregulation of epigenetic processes and disease pathogenesis, particularly in cancer, has led to much interest in identifying drug targets. This prompted the development of small molecule inhibitors, primarily in haematological malignancies. While there have been epigenetic-targeting drugs to receive FDA approval for the treatment of cancers, many suffer from limited applicability, toxicity and the onset of drug resistance, as our understanding of the biology remains incomplete. The recent advent of genome-wide RNAi and CRISPR screens has shed new light on loss of specific proteins causing vulnerabilities of specific cancer types, highlighting the potential for exploiting synthetic lethality as a therapeutic approach. However, small molecule inhibitors have largely been unable to recapitulate phenotypic effects observed using genome-wide knockdown approaches. This mechanistic disconnect and gap are set to be addressed by targeted protein degradation. Degraders such as PROTACs targeting epigenetic proteins recapitulate CRISPR mediated genetic knockdown at the post-translational level and therefore can better exploit target druggability. Here, we review the current landscape of epigenetic drug discovery, the rationale behind and progress made in the development of PROTAC degraders, and look at future perspectives for the field.
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Affiliation(s)
- Thomas Webb
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom
| | - Conner Craigon
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom.
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17
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Bano I, Malhi M, Zhao M, Giurgiulescu L, Sajjad H, Kieliszek M. A review on cullin neddylation and strategies to identify its inhibitors for cancer therapy. 3 Biotech 2022; 12:103. [PMID: 35463041 PMCID: PMC8964847 DOI: 10.1007/s13205-022-03162-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/29/2022] [Indexed: 11/01/2022] Open
Abstract
The cullin-RING E3 ligases (CRLs) are the biggest components of the E3 ubiquitin ligase protein family, and they represent an essential role in various diseases that occur because of abnormal activation, particularly in tumors development. Regulation of CRLs needs neddylation, a post-translational modification involving an enzymatic cascade that transfers small, ubiquitin-like NEDD8 protein to CRLs. Many previous studies have confirmed neddylation as an enticing target for anticancer drug discoveries, and few recent studies have also found a significant increase in advancement in protein neddylation, including preclinical and clinical target validation to discover the neddylation inhibitor compound. In the present review, we first presented briefly the essence of CRLs' neddylation and its control, systematic analysis of CRLs, followed by the description of a few recorded chemical inhibitors of CRLs neddylation enzymes with recent examples of preclinical and clinical targets. We have also listed various structure-based pointing of protein-protein dealings in the CRLs' neddylation reaction, and last, the methods available to discover new inhibitors of neddylation are elaborated. This review will offer a concentrated, up-to-date, and detailed description of the discovery of neddylation inhibitors.
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18
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Jimenez DG, Sebastiano MR, Caron G, Ermondi G. Are we ready to design oral PROTACs®? ADMET AND DMPK 2022; 9:243-254. [PMID: 35300370 PMCID: PMC8920102 DOI: 10.5599/admet.1037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/22/2021] [Indexed: 12/25/2022] Open
Abstract
PROTACs® are expected to strongly impact the future of drug discovery. Therefore, in this work we firstly performed a statistical study to highlight the distribution of E3 ligases and POIs collected in PROTAC-DB, the main online database focused on degraders. Moreover, since the emerging technology of protein degradation deals with large and complex chemical structures, the second part of the paper focuses on how to set up a property-based design strategy to obtain oral degraders. For this purpose, we calculated a pool of seven previously ad hoc selected 2D descriptors for the 2258 publicly available degraders in PROTAC-DB (average values: MW= 972.9 Da, nC= 49.5, NAR= 4.5, PHI= 17.3, nHDon= 4.5, nHAcc= 17.7 and TPSA= 240 Å2) and compared them to a dataset of 50 bRo5 orally approved drugs. Then, a chemical space based on nC, PHI and TPSA was built and subregions with optimal permeability and bioavailability were identified. Bioavailable degraders (ARV-110 and ARV-471) tend to be closer to the Ro5 region, using mainly semi-rigid linkers. Permeable degraders, on the other hand, are placed in an average central region of the chemical space but chameleonicity could allow them to be located closer to the two Arvinas compounds.
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Affiliation(s)
- Diego Garcia Jimenez
- University of Torino, Molecular Biotechnology and Health Sciences Dept., CASSMedChem, via Quarello 15, 10135 Torino, Italy
| | - Matteo Rossi Sebastiano
- University of Torino, Molecular Biotechnology and Health Sciences Dept., CASSMedChem, via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- University of Torino, Molecular Biotechnology and Health Sciences Dept., CASSMedChem, via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- University of Torino, Molecular Biotechnology and Health Sciences Dept., CASSMedChem, via Quarello 15, 10135 Torino, Italy
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19
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Abstract
Targeted protein degradation (TPD) is an emerging therapeutic modality with the potential to tackle disease-causing proteins that have historically been highly challenging to target with conventional small molecules. In the 20 years since the concept of a proteolysis-targeting chimera (PROTAC) molecule harnessing the ubiquitin-proteasome system to degrade a target protein was reported, TPD has moved from academia to industry, where numerous companies have disclosed programmes in preclinical and early clinical development. With clinical proof-of-concept for PROTAC molecules against two well-established cancer targets provided in 2020, the field is poised to pursue targets that were previously considered 'undruggable'. In this Review, we summarize the first two decades of PROTAC discovery and assess the current landscape, with a focus on industry activity. We then discuss key areas for the future of TPD, including establishing the target classes for which TPD is most suitable, expanding the use of ubiquitin ligases to enable precision medicine and extending the modality beyond oncology.
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Affiliation(s)
| | | | - Craig M Crews
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, USA.
- Department of Pharmacology, Yale University, New Haven, CT, USA.
- Department of Chemistry, Yale University, New Haven, CT, USA.
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20
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The NEDD4 ubiquitin E3 ligase: a snapshot view of its functional activity and regulation. Biochem Soc Trans 2022; 50:473-485. [PMID: 35129615 DOI: 10.1042/bst20210731] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 11/17/2022]
Abstract
Due to its fundamental role in all eukaryotic cells, a deeper understanding of the molecular mechanisms underlying ubiquitination is of central importance. Being responsible for chain specificity and substrate recognition, E3 ligases are the selective elements of the ubiquitination process. In this review, we discuss different cellular pathways regulated by one of the first identified E3 ligase, NEDD4, focusing on its pathophysiological role, its known targets and modulators. In addition, we highlight small molecule inhibitors that act on NEDD4 and discuss new strategies to effectively target this E3 enzyme.
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21
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Lv D, Pal P, Liu X, Jia Y, Thummuri D, Zhang P, Hu W, Pei J, Zhang Q, Zhou S, Khan S, Zhang X, Hua N, Yang Q, Arango S, Zhang W, Nayak D, Olsen SK, Weintraub ST, Hromas R, Konopleva M, Yuan Y, Zheng G, Zhou D. Development of a BCL-xL and BCL-2 dual degrader with improved anti-leukemic activity. Nat Commun 2021; 12:6896. [PMID: 34824248 PMCID: PMC8617031 DOI: 10.1038/s41467-021-27210-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 11/05/2021] [Indexed: 02/04/2023] Open
Abstract
PROteolysis-TArgeting Chimeras (PROTACs) have emerged as an innovative drug development platform. However, most PROTACs have been generated empirically because many determinants of PROTAC specificity and activity remain elusive. Through computational modelling of the entire NEDD8-VHL Cullin RING E3 ubiquitin ligase (CRLVHL)/PROTAC/BCL-xL/UbcH5B(E2)-Ub/RBX1 complex, we find that this complex can only ubiquitinate the lysines in a defined band region on BCL-xL. Using this approach to guide our development of a series of ABT263-derived and VHL-recruiting PROTACs, we generate a potent BCL-xL and BCL-2 (BCL-xL/2) dual degrader with significantly improved antitumor activity against BCL-xL/2-dependent leukemia cells. Our results provide experimental evidence that the accessibility of lysines on a target protein plays an important role in determining the selectivity and potency of a PROTAC in inducing protein degradation, which may serve as a conceptual framework to guide the future development of PROTACs.
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Affiliation(s)
- Dongwen Lv
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Pratik Pal
- grid.15276.370000 0004 1936 8091Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Xingui Liu
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Yannan Jia
- grid.240145.60000 0001 2291 4776Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Dinesh Thummuri
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Peiyi Zhang
- grid.15276.370000 0004 1936 8091Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Wanyi Hu
- grid.15276.370000 0004 1936 8091Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Jing Pei
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Qi Zhang
- grid.240145.60000 0001 2291 4776Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Shuo Zhou
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Sajid Khan
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Xuan Zhang
- grid.15276.370000 0004 1936 8091Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Nan Hua
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Qingping Yang
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Sebastian Arango
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Weizhou Zhang
- grid.15276.370000 0004 1936 8091Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL USA
| | - Digant Nayak
- grid.267309.90000 0001 0629 5880Department of Biochemistry & Structure Biology, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880Mays Cancer Center, the Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Shaun K. Olsen
- grid.267309.90000 0001 0629 5880Department of Biochemistry & Structure Biology, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880Mays Cancer Center, the Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Susan T. Weintraub
- grid.267309.90000 0001 0629 5880Department of Biochemistry & Structure Biology, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Robert Hromas
- grid.267309.90000 0001 0629 5880Mays Cancer Center, the Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Marina Konopleva
- grid.240145.60000 0001 2291 4776Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA.
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA.
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA.
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22
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Liu CH, Rao Y, Gao D, Wan L, Zhang L. Editorial: Ubiquitin Code: From Cell Biology to Translational Medicine. Front Cell Dev Biol 2021; 9:791967. [PMID: 34778279 PMCID: PMC8581446 DOI: 10.3389/fcell.2021.791967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Rao
- Ministry of Education Key Laboratory of Protein Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Daming Gao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Lixin Wan
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
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23
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Abstract
Proteolysis-targeting chimeras (PROTACs), which selectively induce targeted protein degradation, represent an emerging drug discovery technology. Although numerous PROTACs have been reported, designing potent PROTACs still remains a great challenge, to some extent, due to insufficient structural data of Target-PROTAC-E3 ternary complexes. In this work, PROTAC-Model, an integrative computational method by combining the FRODOCK-based protocol and RosettaDock-based refinement, was developed to predict PROTAC-mediated ternary complex structures and tested on 14 cases. The quality of the models was evaluated using the criteria of the critical assessment of predicted interactions (CAPRI). Using the unbound structures, the FRODOCK-based protocol can generate the ternary complex structures with medium or high quality for 8 cases out of 14. With the refinement by RosettaDock, the cases with medium or high quality increase to 12. Compared with PRosettaC and the method developed by Drummond et al., PROTAC-Model shows better performance. In summary, PROTAC-Model should be useful for the rational design of PROTACs.
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Affiliation(s)
- Gaoqi Weng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Dan Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou 310058, Zhejiang, China
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24
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Wei D, Wang H, Zeng Q, Wang W, Hao B, Feng X, Wang P, Song N, Kan W, Huang G, Zhou X, Tan M, Zhou Y, Huang R, Li J, Chen XH. Discovery of Potent and Selective CDK9 Degraders for Targeting Transcription Regulation in Triple-Negative Breast Cancer. J Med Chem 2021; 64:14822-14847. [PMID: 34538051 DOI: 10.1021/acs.jmedchem.1c01350] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Triple-negative breast cancer (TNBC) is highly aggressive with very limited treatment options due to the lack of efficient targeted therapies and thus still remains clinically challenging. Targeting transcription-associated cyclin-dependent kinases to remodel transcriptional regulation shows great promise in cancer therapy. Herein, we report the synthesis, optimization, and evaluation of new series of heterobifunctional molecules as highly selective and efficacious CDK9 degraders, enabling potent inhibition of TNBC cell growth and rapidly targeted degradation of CDK9. Moreover, the most potent CDK9 degrader (compound 45) induces cell apoptosis in vitro and inhibits tumor growth in the MDA-MB-231 TNBC model. Furthermore, the RNA-seq, immunohistochemistry assays demonstrate that the CDK9 degrader downregulates the downstream targets, such as MYC, at the transcriptional level, resulting apoptosis in TNBC cells. Our work establishes that 45 is a highly potent and efficacious CDK9 degrader for targeting transcription regulation, which represents an effective strategy and great potential as a new targeted therapy for TNBC.
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Affiliation(s)
- Dan Wei
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanlin Wang
- College of Pharmacy, Fudan University, Shanghai 201203, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinghe Zeng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjing Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xule Feng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Peipei Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ning Song
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijuan Kan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Guifang Huang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaoyu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yubo Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Zhongshan Institute for Drug Discovery, The Institutes of Drug Discovery and Development, CAS, Zhongshan, Guangdong 528400, China
| | - Ruimin Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jia Li
- College of Pharmacy, Fudan University, Shanghai 201203, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Zhongshan Institute for Drug Discovery, The Institutes of Drug Discovery and Development, CAS, Zhongshan, Guangdong 528400, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xiao-Hua Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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25
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Bastien J, Menon S, Messa M, Nyfeler B. Molecular targets and approaches to restore autophagy and lysosomal capacity in neurodegenerative disorders. Mol Aspects Med 2021; 82:101018. [PMID: 34489092 DOI: 10.1016/j.mam.2021.101018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 01/18/2023]
Abstract
Autophagy is a catabolic process that promotes cellular fitness by clearing aggregated protein species, pathogens and damaged organelles through lysosomal degradation. The autophagic process is particularly important in the nervous system where post-mitotic neurons rely heavily on protein and organelle quality control in order to maintain cellular health throughout the lifetime of the organism. Alterations of autophagy and lysosomal function are hallmarks of various neurodegenerative disorders. In this review, we conceptualize some of the mechanistic and genetic evidence pointing towards autophagy and lysosomal dysfunction as a causal driver of neurodegeneration. Furthermore, we discuss rate-limiting pathway nodes and potential approaches to restore pathway activity, from autophagy initiation, cargo sequestration to lysosomal capacity.
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Affiliation(s)
- Julie Bastien
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Suchithra Menon
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Mirko Messa
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Beat Nyfeler
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
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26
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Rodriguez-Rivera FP, Levi SM. Unifying Catalysis Framework to Dissect Proteasomal Degradation Paradigms. ACS CENTRAL SCIENCE 2021; 7:1117-1125. [PMID: 34345664 PMCID: PMC8323112 DOI: 10.1021/acscentsci.1c00389] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Indexed: 06/13/2023]
Abstract
Diverging from traditional target inhibition, proteasomal protein degradation approaches have emerged as novel therapeutic modalities that embody distinct pharmacological profiles and can access previously undrugged targets. Small molecule degraders have the potential to catalytically destroy target proteins at substoichiometric concentrations, thus lowering administered doses and extending pharmacological effects. With this mechanistic premise, research efforts have advanced the development of small molecule degraders that benefit from stable and increased affinity ternary complexes. However, a holistic framework that evaluates different degradation modes from a catalytic perspective, including focusing on kinetically favored degradation mechanisms, is lacking. In this Outlook, we introduce the concept of an induced cooperativity spectrum as a unifying framework to mechanistically understand catalytic degradation profiles. This framework is bolstered by key examples of published molecular degraders extending from molecular glues to bivalent degraders. Critically, we discuss remaining challenges and future opportunities in drug discovery to rationally design and phenotypically screen for efficient degraders.
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Affiliation(s)
- Frances P. Rodriguez-Rivera
- Discovery
Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Samuel M. Levi
- Pfizer
Worldwide Research and Development, Pfizer,
Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
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27
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Cresser-Brown JO, Marsh GP, Maple HJ. Reviewing the toolbox for degrader development in oncology. Curr Opin Pharmacol 2021; 59:43-51. [PMID: 34058637 DOI: 10.1016/j.coph.2021.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022]
Abstract
The field of targeted protein degradation encompasses a growing number of modalities that achieve potent and selective knockdown of target proteins at the post-translational level. Among the most clinically advanced are bifunctional small-molecule degraders, also referred to as PROteolysis Targeting Chimeras, Degronimids, SNIPERs, or uSMITEs. Although applicable to many disease indications, oncology stands to be the first to benefit from this promising therapeutic approach, with the first investigational new drugs (INDs) filed in 2019 and a proliferation of research specifically focused on harnessing degraders for cancer treatment. In this review, we consider the toolbox of guidelines, reagents, and technologies that has evolved alongside the field to support degrader research and development.
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Affiliation(s)
- Joel O Cresser-Brown
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol, UK
| | - Graham P Marsh
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol, UK
| | - Hannah J Maple
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol, UK.
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28
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Kannt A, Đikić I. Expanding the arsenal of E3 ubiquitin ligases for proximity-induced protein degradation. Cell Chem Biol 2021; 28:1014-1031. [PMID: 33945791 DOI: 10.1016/j.chembiol.2021.04.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022]
Abstract
Efficacy and selectivity of molecules inducing protein degradation depend on their affinity to the target protein but also on the type of E3 ubiquitin ligase that is recruited to trigger proteasomal degradation. While tremendous progress has been made on the former, the latter-the arsenal of E3 ligases that can be hijacked for targeted protein degradation-is still largely unexplored. Only about 2% of the more than 600 E3 ligases have been utilized to date. Exploiting additional E3 ligases that are, for example, selectively expressed in specific tissues or cells, or regulated under certain conditions, can considerably broaden the applicability of molecular degraders as a therapeutic modality. Here, we provide an overview of major classes of E3 ligases, review the enzymes that have been exploited for induced protein degradation and approaches used to identify or design E3 ligands, and highlight challenges and opportunities for targeting new E3 ligases.
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Affiliation(s)
- Aimo Kannt
- Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute of Clinical Pharmacology, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Ivan Đikić
- Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany.
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29
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Jevtić P, Haakonsen DL, Rapé M. An E3 ligase guide to the galaxy of small-molecule-induced protein degradation. Cell Chem Biol 2021; 28:1000-1013. [PMID: 33891901 DOI: 10.1016/j.chembiol.2021.04.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/28/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022]
Abstract
Induced protein degradation accomplishes elimination, rather than inhibition, of pathological proteins. Key to the success of this novel therapeutic modality is the modification of proteins with ubiquitin chains, which is brought about by molecular glues or bivalent compounds that induce proximity between the target protein and an E3 ligase. The human genome encodes ∼600 E3 ligases that differ widely in their structures, catalytic mechanisms, modes of regulation, and physiological roles. While many of these enzymes hold great promise for drug discovery, few have been successfully engaged by small-molecule degraders. Here, we review E3 ligases that are being used for induced protein degradation. Based on these prior successes and our growing understanding of the biology and biochemistry of E3 ligases, we propose new ubiquitylation enzymes that can be harnessed for drug discovery to firmly establish induced protein degradation as a specific and efficient therapeutic approach.
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Affiliation(s)
- Predrag Jevtić
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Diane L Haakonsen
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Michael Rapé
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.
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