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Expert Opinion on Drug Discovery Apr 2023Target protein degradation (TPD) provides a novel therapeutic modality, other than inhibition, through the direct depletion of target proteins. Two primary human protein... (Review)
Review
INTRODUCTION
Target protein degradation (TPD) provides a novel therapeutic modality, other than inhibition, through the direct depletion of target proteins. Two primary human protein homeostasis mechanisms are exploited: the ubiquitin-proteasome system (UPS) and the lysosomal system. TPD technologies based on these two systems are progressing at an impressive pace.
AREAS COVERED
This review focuses on the TPD strategies based on UPS and lysosomal system, mainly classified into three types: Molecular Glue (MG), PROteolysis Targeting Chimera (PROTAC), and lysosome-mediated TPD. Starting with a brief background introduction of each strategy, exciting examples and perspectives on these novel approaches are provided.
EXPERT OPINION
MGs and PROTACs are two major UPS-based TPD strategies that have been extensively investigated in the past decade. Despite some clinical trials, several critical issues remain, among which is emphasized by the limitation of targets. Recently developed lysosomal system-based approaches provide alternative solutions for TPD beyond UPS' capability. The newly emerging novel approaches may partially address issues that have long plagued researchers, such as low potency, poor cell permeability, on-/off-target toxicity, and delivery efficiency. Comprehensive considerations for the rational design of protein degraders and continuous efforts to seek effective solutions are imperative to advance these strategies into clinical medications.
Topics: Humans; Proteolysis; Drug Discovery; Permeability; Proteolysis Targeting Chimera; Research Personnel
PubMed: 36895136
DOI: 10.1080/17460441.2023.2187777 -
Nature Communications Sep 2022Conditional degron tags (CDTs) are a powerful tool for target validation that combines the kinetics and reversible action of pharmacological agents with the...
Conditional degron tags (CDTs) are a powerful tool for target validation that combines the kinetics and reversible action of pharmacological agents with the generalizability of genetic manipulation. However, successful design of a CDT fusion protein often requires a prolonged, ad hoc cycle of construct design, failure, and re-design. To address this limitation, we report here a system to rapidly compare the activity of five unique CDTs: AID/AID2, IKZF3d, dTAG, HaloTag, and SMASh. We demonstrate the utility of this system against 16 unique protein targets. We find that expression and degradation are highly dependent on the specific CDT, the construct design, and the target. None of the CDTs leads to efficient expression and/or degradation across all targets; however, our systematic approach enables the identification of at least one optimal CDT fusion for each target. To enable the adoption of CDT strategies more broadly, we have made these reagents, and a detailed protocol, available as a community resource.
Topics: Kinetics; Proteolysis
PubMed: 36127368
DOI: 10.1038/s41467-022-33246-4 -
Biomolecules Nov 2021The proteasome system is a large and complex molecular machinery responsible for the degradation of misfolded, damaged, and redundant cellular proteins. When proteasome... (Review)
Review
The proteasome system is a large and complex molecular machinery responsible for the degradation of misfolded, damaged, and redundant cellular proteins. When proteasome function is impaired, unwanted proteins accumulate, which can lead to several diseases including age-related and neurodegenerative diseases. Enhancing proteasome-mediated substrate degradation with small molecules may therefore be a valuable strategy for the treatment of various neurodegenerative diseases such as Parkinson's, Alzheimer's, and Huntington's diseases. In this review, we discuss the structure of proteasome and how proteasome's proteolytic activity is associated with aging and various neurodegenerative diseases. We also summarize various classes of compounds that are capable of enhancing, directly or indirectly, proteasome-mediated protein degradation.
Topics: Aging; Humans; Neurodegenerative Diseases; Proteasome Endopeptidase Complex; Proteasome Inhibitors; Protein Folding; Proteolysis; Small Molecule Libraries
PubMed: 34944433
DOI: 10.3390/biom11121789 -
The FEBS Journal May 2020Proteases play critical roles in virtually all biological processes, including proliferation, cell death and survival, protein turnover, and migration. However, when... (Review)
Review
Proteases play critical roles in virtually all biological processes, including proliferation, cell death and survival, protein turnover, and migration. However, when dysregulated, these enzymes contribute to the progression of multiple diseases, with cancer, neurodegenerative disorders, inflammation, and blood disorders being the most prominent examples. For a long time, disease-associated proteases have been used for the activation of various prodrugs due to their well-characterized catalytic activity and ability to selectively cleave only those substrates that strictly correspond with their active site architecture. To date, versatile peptide sequences that are cleaved by proteases in a site-specific manner have been utilized as bioactive linkers for the targeted delivery of multiple types of cargo, including fluorescent dyes, photosensitizers, cytotoxic drugs, antibiotics, and pro-antibodies. This platform is highly adaptive, as multiple protease-labile conjugates have already been developed, some of which are currently in clinical use for cancer treatment. In this review, recent advancements in the development of novel protease-cleavable linkers for selective drug delivery are described. Moreover, the current limitations regarding the selectivity of linkers are discussed, and the future perspectives that rely on the application of unnatural amino acids for the development of highly selective peptide linkers are also presented.
Topics: Catalysis; Catalytic Domain; Drug Delivery Systems; Humans; Peptide Hydrolases; Peptides; Prodrugs; Proteolysis
PubMed: 31991521
DOI: 10.1111/febs.15227 -
Cell Reports Jul 2023The 26S proteasome comprises 20S catalytic and 19S regulatory complexes. Approximately half of the proteasomes in cells exist as free 20S complexes; however, our...
The 26S proteasome comprises 20S catalytic and 19S regulatory complexes. Approximately half of the proteasomes in cells exist as free 20S complexes; however, our mechanistic understanding of what determines the ratio of 26S to 20S species remains incomplete. Here, we show that glucose starvation uncouples 26S holoenzymes into 20S and 19S subcomplexes. Subcomplex affinity purification and quantitative mass spectrometry reveal that Ecm29 proteasome adaptor and scaffold (ECPAS) mediates this structural remodeling. The loss of ECPAS abrogates 26S dissociation, reducing degradation of 20S proteasome substrates, including puromycylated polypeptides. In silico modeling suggests that ECPAS conformational changes commence the disassembly process. ECPAS is also essential for endoplasmic reticulum stress response and cell survival during glucose starvation. In vivo xenograft model analysis reveals elevated 20S proteasome levels in glucose-deprived tumors. Our results demonstrate that the 20S-19S disassembly is a mechanism adapting global proteolysis to physiological needs and countering proteotoxic stress.
Topics: Humans; Proteasome Endopeptidase Complex; Cytoplasm; Proteolysis; Mass Spectrometry
PubMed: 37384533
DOI: 10.1016/j.celrep.2023.112701 -
Angewandte Chemie (International Ed. in... May 2021Proteolysis of proteins and peptides is involved in the infection of cells by enveloped viruses and also in the invasion and spread of cancer cells. Shutting down...
Proteolysis of proteins and peptides is involved in the infection of cells by enveloped viruses and also in the invasion and spread of cancer cells. Shutting down broad-specificity proteases, however, is problematic because normal functions by these proteases will be affected. Herein, nanoparticle receptors were prepared from molecular imprinting for complex biological peptides. Their strong and selective binding enabled them to protect their targeted sequences from proteolysis in aqueous solution at stoichiometric amounts. Generality of the method was demonstrated by the protection of hydrophobic and hydrophilic peptides from different proteases, selective protection of a segment of a long peptide, and selective protection of a targeted peptide in a mixture. Most interestingly, two receptors targeting different parts of a long peptide could work in cooperation to protect the overall sequence, highlighting the versatility of the method.
Topics: Peptide Hydrolases; Peptides; Proteolysis
PubMed: 33725413
DOI: 10.1002/anie.202102148 -
Journal of the American Chemical Society Feb 2023Only around 20% of the human proteome is considered to be druggable with small-molecule antagonists. This leaves some of the most compelling therapeutic targets outside... (Review)
Review
Only around 20% of the human proteome is considered to be druggable with small-molecule antagonists. This leaves some of the most compelling therapeutic targets outside the reach of ligand discovery. The concept of targeted protein degradation (TPD) promises to overcome some of these limitations. In brief, TPD is dependent on small molecules that induce the proximity between a protein of interest (POI) and an E3 ubiquitin ligase, causing ubiquitination and degradation of the POI. In this perspective, we want to reflect on current challenges in the field, and discuss how advances in multiomics profiling, artificial intelligence, and machine learning (AI/ML) will be vital in overcoming them. The presented roadmap is discussed in the context of small-molecule degraders but is equally applicable for other emerging proximity-inducing modalities.
Topics: Humans; Artificial Intelligence; Multiomics; Proteolysis; Ubiquitin-Protein Ligases; Ubiquitination
PubMed: 36706315
DOI: 10.1021/jacs.2c11098 -
Journal of the American Chemical Society Aug 2023Protein dysregulation has been characterized as the cause of pathogenesis in many different diseases. For proteins lacking easily druggable pockets or catalytically...
Protein dysregulation has been characterized as the cause of pathogenesis in many different diseases. For proteins lacking easily druggable pockets or catalytically active sites, targeted protein degradation is an attractive therapeutic approach. While several methods for targeted protein degradation have been developed, there remains a demand for lower molecular weight molecules that promote efficient degradation of their targets. In this work, we describe the synthesis and validation of a series of heterobifunctional molecules that bind a protein of interest through a small molecule ligand while targeting them to the lysosome using a short gluten peptide that leverages the TG2/LRP-1 pathway. We demonstrate that this approach can be used to effectively endocytose and degrade representative secreted, cell surface, and transmembrane proteins, notably streptavidin, the vitamin B12 receptor, cubilin, and integrin αβ. Optimization of these prototypical molecules could generate pharmacologically relevant LYTAC agents.
Topics: Membrane Proteins; Biological Transport; Proteolysis; Cell Membrane; Lysosomes
PubMed: 37590164
DOI: 10.1021/jacs.3c05109 -
Nucleus (Austin, Tex.) Dec 2019The nucleus is enclosed by a double-membrane structure, the nuclear envelope, which separates the nucleoplasm from the cytoplasm. The outer nuclear membrane is... (Review)
Review
The nucleus is enclosed by a double-membrane structure, the nuclear envelope, which separates the nucleoplasm from the cytoplasm. The outer nuclear membrane is continuous with the endoplasmic reticulum (ER), whereas the inner nuclear membrane (INM) is a specialized compartment with a unique proteome. In order to ensure compartmental homeostasis, INM-associated degradation (INMAD) is required for both protein quality control and regulated proteolysis of INM proteins. INMAD shares similarities with ER-associated degradation (ERAD). The mechanism of ERAD is well characterized, whereas the INMAD pathway requires further definition. Here we review the three different branches of INMAD, mediated by their respective E3 ubiquitin ligases: Doa10, Asi1-3, and APC/C. We clarify the distinction between ERAD and INMAD, their substrate recognition signals, and the subsequent processing by their respective degradation machineries. We also discuss the significance of cell-cycle and developmental regulation of protein clearance at the INM, and its relationship to human disease.
Topics: Animals; Humans; Membrane Proteins; Nuclear Envelope; Proteolysis
PubMed: 31313624
DOI: 10.1080/19491034.2019.1644593 -
Mechanisms of Ageing and Development Oct 2023Iron is the most abundant trace element in the human body. Since iron can switch between its 2-valent and 3-valent form it is essential in various physiological... (Review)
Review
Iron is the most abundant trace element in the human body. Since iron can switch between its 2-valent and 3-valent form it is essential in various physiological processes such as energy production, proliferation or DNA synthesis. Especially high metabolic organs such as the heart rely on iron-associated iron-sulfur and heme proteins. However, due to switches in iron oxidation state, iron overload exhibits high toxicity through formation of reactive oxygen species, underlining the importance of balanced iron levels. Growing evidence demonstrates disturbance of this balance during aging. While age-associated cardiovascular diseases are often related to iron deficiency, in physiological aging cardiac iron accumulates. To understand these changes, we focused on inflammation and proteolysis, two hallmarks of aging, and their role in iron metabolism. Via the IL-6-hepcidin axis, inflammation and iron status are strongly connected often resulting in anemia accompanied by infiltration of macrophages. This tight connection between anemia and inflammation highlights the importance of the macrophage iron metabolism during inflammation. Age-related decrease in proteolytic activity additionally affects iron balance due to impaired degradation of iron metabolism proteins. Therefore, this review accentuates alterations in iron metabolism during aging with regards to inflammation and proteolysis to draw attention to their implications and associations.
Topics: Humans; Iron; Proteolysis; Anemia; Inflammation; Aging
PubMed: 37678569
DOI: 10.1016/j.mad.2023.111869