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Chemical Society Reviews Jun 2022Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules consisting of one ligand that binds to a protein of interest (POI) and another that can recruit... (Review)
Review
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules consisting of one ligand that binds to a protein of interest (POI) and another that can recruit an E3 ubiquitin ligase. The chemically-induced proximity between the POI and E3 ligase results in ubiquitination and subsequent degradation of the POI by the ubiquitin-proteasome system (UPS). The event-driven mechanism of action (MOA) of PROTACs offers several advantages compared to traditional occupancy-driven small molecule inhibitors, such as a catalytic nature, reduced dosing and dosing frequency, a more potent and longer-lasting effect, an added layer of selectivity to reduce potential toxicity, efficacy in the face of drug-resistance mechanisms, targeting nonenzymatic functions, and expanded target space. Here, we highlight important milestones and briefly discuss lessons learned about targeted protein degradation (TPD) in recent years and conjecture on the efforts still needed to expand the toolbox for PROTAC discovery to ultimately provide promising therapeutics.
Topics: Proteasome Endopeptidase Complex; Proteolysis; Ubiquitin-Protein Ligases; Ubiquitination
PubMed: 35671157
DOI: 10.1039/d2cs00193d -
Nature Chemical Biology Jan 2023Engineered destruction of target proteins by recruitment to the cell's degradation machinery has emerged as a promising strategy in drug discovery. The majority of...
Engineered destruction of target proteins by recruitment to the cell's degradation machinery has emerged as a promising strategy in drug discovery. The majority of molecules that facilitate targeted degradation do so via a select number of ubiquitin ligases, restricting this therapeutic approach to tissue types that express the requisite ligase. Here, we describe a new strategy of targeted protein degradation through direct substrate recruitment to the 26S proteasome. The proteolytic complex is essential and abundantly expressed in all cells; however, proteasomal ligands remain scarce. We identify potent peptidic macrocycles that bind directly to the 26S proteasome subunit PSMD2, with a 2.5-Å-resolution cryo-electron microscopy complex structure revealing a binding site near the 26S pore. Conjugation of this macrocycle to a potent BRD4 ligand enabled generation of chimeric molecules that effectively degrade BRD4 in cells, thus demonstrating that degradation via direct proteasomal recruitment is a viable strategy for targeted protein degradation.
Topics: Nuclear Proteins; Cryoelectron Microscopy; Transcription Factors; Proteasome Endopeptidase Complex; Proteolysis; Ligases; Ubiquitin-Protein Ligases
PubMed: 36577875
DOI: 10.1038/s41589-022-01218-w -
FEBS Letters Jun 2005The 26S proteasome is responsible for regulated proteolysis of most intracellular proteins yet the focus of intense regulatory action itself. Proteasome abundance is... (Review)
Review
The 26S proteasome is responsible for regulated proteolysis of most intracellular proteins yet the focus of intense regulatory action itself. Proteasome abundance is responsive to cell needs or stress conditions, and dynamically localized to concentrations of substrates. Proteasomes are continually assembled and disassembled, and their subunits subject to a variety of posttranslational modifications. Furthermore, as robust and multi-tasking as this complex is, it does not function alone. A spattering of closely associating proteins enhances complex stability, fine-tunes activity, assists in substrate-binding, recycling of ubiquitin, and more. HEAT repeat caps activate proteasomes, yet share remarkable features with nuclear importins. Fascinating cross talk even occurs with ribosomes through common maturation factors. The dynamics of proteasome configurations and how they relate to diverse activities is the topic of this review.
Topics: Animals; Humans; Proteasome Endopeptidase Complex; Protein Binding; Protein Transport; Ribosomes
PubMed: 15890341
DOI: 10.1016/j.febslet.2005.04.048 -
Biochimica Et Biophysica Acta Jan 2014Most proteasome substrates are marked for degradation by ubiquitin conjugation, but some are targeted by other means. The properties of these exceptional cases provide... (Review)
Review
Most proteasome substrates are marked for degradation by ubiquitin conjugation, but some are targeted by other means. The properties of these exceptional cases provide insights into the general requirements for proteasomal degradation. Here the focus is on three ubiquitin-independent substrates that have been the subject of detailed study. These are Rpn4, a transcriptional regulator of proteasome homeostasis, thymidylate synthase, an enzyme required for production of DNA precursors and ornithine decarboxylase, the initial enzyme committed to polyamine biosynthesis. It can be inferred from these cases that proteasome association and the presence of an unstructured region are the sole prerequisites for degradation. Based on that inference, artificial substrates have been designed to test the proteasome's capacity for substrate processing and its limitations. Ubiquitin-independent substrates may in some cases be a remnant of the pre-ubiquitome world, but in other cases could provide optimized regulatory solutions. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
Topics: Animals; DNA-Binding Proteins; Humans; Ornithine Decarboxylase; Proteasome Endopeptidase Complex; Protein Structure, Tertiary; Protein Unfolding; Proteolysis; Saccharomyces cerevisiae Proteins; Thymidylate Synthase; Transcription Factors; Ubiquitin
PubMed: 23684952
DOI: 10.1016/j.bbamcr.2013.05.008 -
Biomolecules Jun 2014Proteasomes are key proteases involved in a variety of processes ranging from the clearance of damaged proteins to the presentation of antigens to CD8+ T-lymphocytes.... (Review)
Review
Proteasomes are key proteases involved in a variety of processes ranging from the clearance of damaged proteins to the presentation of antigens to CD8+ T-lymphocytes. Which cleavage sites are used within the target proteins and how fast these proteins are degraded have a profound impact on immune system function and many cellular metabolic processes. The regulation of proteasome activity involves different mechanisms, such as the substitution of the catalytic subunits, the binding of regulatory complexes to proteasome gates and the proteasome conformational modifications triggered by the target protein itself. Mathematical models are invaluable in the analysis; and potentially allow us to predict the complex interactions of proteasome regulatory mechanisms and the final outcomes of the protein degradation rate and MHC class I epitope generation. The pioneering attempts that have been made to mathematically model proteasome activity, cleavage preference variation and their modification by one of the regulatory mechanisms are reviewed here.
Topics: Animals; Humans; Hydrolysis; Models, Biological; Oligopeptides; Proteasome Endopeptidase Complex
PubMed: 24970232
DOI: 10.3390/biom4020585 -
Biomolecules Aug 2023The 26S proteasome is the largest and most complicated protease known, and changes to proteasome assembly or function contribute to numerous human diseases. Assembly of... (Review)
Review
The 26S proteasome is the largest and most complicated protease known, and changes to proteasome assembly or function contribute to numerous human diseases. Assembly of the 26S proteasome from its ~66 individual polypeptide subunits is a highly orchestrated process requiring the concerted actions of both intrinsic elements of proteasome subunits, as well as assistance by extrinsic, dedicated proteasome assembly chaperones. With the advent of near-atomic resolution cryo-electron microscopy, it has become evident that the proteasome is a highly dynamic machine, undergoing numerous conformational changes in response to ligand binding and during the proteolytic cycle. In contrast, an appreciation of the role of conformational dynamics during the biogenesis of the proteasome has only recently begun to emerge. Herein, we review our current knowledge of proteasome assembly, with a particular focus on how conformational dynamics guide particular proteasome biogenesis events. Furthermore, we highlight key emerging questions in this rapidly expanding area.
Topics: Proteasome Endopeptidase Complex; Protein Conformation; Models, Molecular; Molecular Chaperones; Humans; Cryoelectron Microscopy; Proteolysis; Ubiquitin
PubMed: 37627288
DOI: 10.3390/biom13081223 -
Biomolecular Concepts Aug 2016The proteasome is a structural complex of many proteins that degrades substrates marked by covalent linkage to ubiquitin. Many years of research has shown a role for... (Review)
Review
The proteasome is a structural complex of many proteins that degrades substrates marked by covalent linkage to ubiquitin. Many years of research has shown a role for ubiquitin-proteasome-mediated proteolysis in synaptic plasticity and memory mainly in degrading synaptic, cytoplasmic and nuclear proteins. Recent work indicates that the proteasome has wider proteolytic and non-proteolytic roles in processes such as histone modifications that affect synaptic plasticity and memory. In this review, we assess the evidence gathered from neuronal as well as non-neuronal cell types regarding the function of the proteasome in positive or negative regulation of posttranslational modifications of histones, such as acetylation, methylation and ubiquitination. We discuss the critical roles of the proteasome in clearing excess histone proteins in various cellular contexts and the possible non-proteolytic functions in regulating transcription of target genes. In addition, we summarize the current literature on diverse chromatin-remodeling machineries, such as histone acetyltransferases, deacetylates, methyltransferases and demethylases, as targets for proteasomal degradation across experimental models. Lastly, we provide a perspective on how proteasomal regulation of histone modifications may modulate synaptic plasticity in the nervous system.
Topics: Animals; DNA Methylation; Epigenesis, Genetic; Epigenomics; Gene Expression Regulation; Gene Silencing; Histones; Humans; Neuronal Plasticity; Proteasome Endopeptidase Complex; Protein Binding; Protein Processing, Post-Translational; Proteolysis; Signal Transduction; Transcription, Genetic; Ubiquitin
PubMed: 27522625
DOI: 10.1515/bmc-2016-0016 -
FEBS Letters Jun 2007In the ubiquitin-proteasome system, substrates fated for destruction first acquire covalent modification by ubiquitin, and are subsequently destroyed by the proteasome.... (Review)
Review
In the ubiquitin-proteasome system, substrates fated for destruction first acquire covalent modification by ubiquitin, and are subsequently destroyed by the proteasome. Traditionally, 26S proteasomes have been seen as largely uniform in their composition and functional capacity. Accordingly, cells can control proteasome abundance via transcriptional pathways that mediate concerted regulation of all known proteasome genes. However, recent evidence suggests that the proteasome is also subject to subunit-specific modes of regulation, which serve to alter proteasome function and may generate ensembles of compositionally distinct proteasomes. These modes of proteasome regulation provide varied means to adapt protein degradation pathways to changing conditions in the cell.
Topics: Animals; Arsenites; DNA-Binding Proteins; Endopeptidases; Humans; Models, Biological; Models, Molecular; Multiprotein Complexes; Proteasome Endopeptidase Complex; RNA-Binding Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Transcription Factors; Transcriptional Activation; Ubiquitin
PubMed: 17418826
DOI: 10.1016/j.febslet.2007.03.053 -
Biochimica Et Biophysica Acta. Gene... Jun 2023A moonlighting protein is one, which carries out multiple, often wholly unrelated, functions. The RAD23 protein is a fascinating example of this, where the same... (Review)
Review
A moonlighting protein is one, which carries out multiple, often wholly unrelated, functions. The RAD23 protein is a fascinating example of this, where the same polypeptide and the embedded domains function independently in both nucleotide excision repair (NER) and protein degradation via the ubiquitin-proteasome system (UPS). Hence, through direct binding to the central NER component XPC, RAD23 stabilizes XPC and contributes to DNA damage recognition. Conversely, RAD23 also interacts directly with the 26S proteasome and ubiquitylated substrates to mediate proteasomal substrate recognition. In this function, RAD23 activates the proteolytic activity of the proteasome and engages specifically in well-characterized degradation pathways through direct interactions with E3 ubiquitin-protein ligases and other UPS components. Here, we summarize the past 40 years of research into the roles of RAD23 in NER and the UPS.
Topics: Proteasome Endopeptidase Complex; Proteolysis; Saccharomyces cerevisiae Proteins; DNA-Binding Proteins; Mutation; DNA Repair; Ubiquitin
PubMed: 36863450
DOI: 10.1016/j.bbagrm.2023.194925 -
Cellular and Molecular Life Sciences :... Sep 2016The ability of ubiquitin to form up to eight different polyubiquitin chain linkages generates complexity within the ubiquitin proteasome system, and accounts for the... (Review)
Review
The ability of ubiquitin to form up to eight different polyubiquitin chain linkages generates complexity within the ubiquitin proteasome system, and accounts for the diverse roles of ubiquitination within the cell. Understanding how each type of ubiquitin linkage is correctly interpreted by ubiquitin binding proteins provides important insights into the link between chain recognition and cellular fate. A major function of ubiquitination is to signal degradation of intracellular proteins by the 26S proteasome. Lysine-48 (K48) linked polyubiquitin chains are well established as the canonical signal for proteasomal degradation, but recent studies show a role for other ubiquitin linked chains in facilitating degradation by the 26S proteasome. Here, we review how different types of polyubiquitin linkage bind to ubiquitin receptors on the 26S proteasome, how they signal degradation and discuss the implications of ubiquitin chain linkage in regulating protein breakdown by the proteasome.
Topics: Humans; Polyubiquitin; Proteasome Endopeptidase Complex; Protein Binding; Ubiquitin; Ubiquitinated Proteins
PubMed: 27137187
DOI: 10.1007/s00018-016-2255-5