-
Frontiers in Immunology 2022Proteasome generates spliced peptides by ligating two distant cleavage products in a reverse proteolysis reaction. The observation that CD8+ T cells recognizing a... (Review)
Review
Proteasome generates spliced peptides by ligating two distant cleavage products in a reverse proteolysis reaction. The observation that CD8+ T cells recognizing a spliced peptide induced T cell rejection in a melanoma patient following adoptive T cell transfer (ATT), raised some hopes with regard to the general therapeutic and immune relevance of spliced peptides. Concomitantly, the identification of spliced peptides was also the start of a controversy with respect to their frequency, abundancy and their therapeutic applicability. Here I review some of the recent evidence favoring or disfavoring an immune relevance of splicetopes and discuss from a theoretical point of view the potential usefulness of tumor specific splicetopes and why against all odds it still may seem worth trying to identify such tumor and patient-specific neosplicetopes for application in ATT.
Topics: CD8-Positive T-Lymphocytes; Humans; Melanoma; Peptides; Proteasome Endopeptidase Complex; Proteolysis
PubMed: 35265089
DOI: 10.3389/fimmu.2022.849863 -
Molecules (Basel, Switzerland) Aug 2021Proteases play a central role in various biochemical pathways catalyzing and regulating key biological events. Proteases catalyze an irreversible post-translational... (Review)
Review
Proteases play a central role in various biochemical pathways catalyzing and regulating key biological events. Proteases catalyze an irreversible post-translational modification called proteolysis by hydrolyzing peptide bonds in proteins. Given the destructive potential of proteolysis, protease activity is tightly regulated. Dysregulation of protease activity has been reported in numerous disease conditions, including cancers, neurodegenerative diseases, inflammatory conditions, cardiovascular diseases, and viral infections. The proteolytic profile of a cell, tissue, or organ is governed by protease activation, activity, and substrate specificity. Thus, identifying protease substrates and proteolytic events under physiological conditions can provide crucial information about how the change in protease regulation can alter the cellular proteolytic landscape. In recent years, mass spectrometry-based techniques called N-terminomics have become instrumental in identifying protease substrates from complex biological mixtures. N-terminomics employs the labeling and enrichment of native and neo-N-termini peptides, generated upon proteolysis followed by mass spectrometry analysis allowing protease substrate profiling directly from biological samples. In this review, we provide a brief overview of N-terminomics techniques, focusing on their strengths, weaknesses, limitations, and providing specific examples where they were successfully employed to identify protease substrates in vivo and under physiological conditions. In addition, we explore the current trends in the protease field and the potential for future developments.
Topics: Humans; Mass Spectrometry; Peptide Hydrolases; Peptides; Proteolysis; Proteomics; Substrate Specificity
PubMed: 34361849
DOI: 10.3390/molecules26154699 -
Biochimica Et Biophysica Acta.... Jan 2022Although interleukin-11 (IL-11) was discovered more than 30 years ago, it remains an understudied member of the IL-6 family of cytokines. While it was originally... (Review)
Review
Although interleukin-11 (IL-11) was discovered more than 30 years ago, it remains an understudied member of the IL-6 family of cytokines. While it was originally discovered as a secreted factor that could foster megakaryocyte maturation and was therefore used as a recombinant protein to increase platelet production in patients with thrombocytopenia, recent research has established important roles for IL-11 in inflammation, fibrosis and cancer. In order to initiate signal transduction, IL-11 binds first to a non-signaling membrane-bound IL-11 receptor (IL-11R, classic signaling), which subsequently induces the formation of a heterodimer of the signal-transducing receptor gp130 that is shared with the other family members. Complex formation initiates several intracellular signaling cascades, most notably the Janus kinase/Signal Transducer and Activator of Transcription (Jak/STAT) pathway. We have recently identified a trans-signaling mechanism, in which IL-11 binds to soluble forms of the IL-11R (sIL-11R) and the agonistic IL-11/sIL-11R complex can activate cells that do not express the IL-11R and would usually not respond to IL-11. The generation of sIL-11R and thus the initiation of IL-11 trans-signaling is mediated by proteolytic cleavage. In this review, we summarize the current state of knowledge regarding IL-11R cleavage, highlight recent developments in IL-11 biology and discuss therapeutic opportunities and challenges in the light of IL-11 classic and trans-signaling.
Topics: Animals; Humans; Interleukin-11; Proteolysis; Receptors, Interleukin-11; Signal Transduction
PubMed: 34624437
DOI: 10.1016/j.bbamcr.2021.119135 -
Current Opinion in Chemical Biology Aug 2020Proteolysis targeting chimeras (PROTACs) are heterobifunctional molecules and allow selective protein degradation by addressing the natural ubiquitin proteasome system.... (Review)
Review
Proteolysis targeting chimeras (PROTACs) are heterobifunctional molecules and allow selective protein degradation by addressing the natural ubiquitin proteasome system. As this new strategy of chemically induced protein degradation can serve as a biological tool and provides new possibilities for drug discovery, it has been applied to a variety of targets including (nuclear) receptors, kinases, and epigenetic proteins. A lot of PROTACs have already been designed in the field of epigenetics, and their synthesis and characterization highly contributed to structural optimization and improved mechanistic understanding of these molecules. In this review, we will discuss and summarize recent advances in PROTAC discovery with focus on epigenetic targets.
Topics: Animals; Drug Discovery; Epigenesis, Genetic; Epigenomics; Humans; Models, Molecular; Molecular Targeted Therapy; Proteasome Endopeptidase Complex; Proteolysis; Ubiquitin
PubMed: 32146413
DOI: 10.1016/j.cbpa.2020.01.010 -
Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation.Nature Communications Jul 2023Targeted protein degradation via "hijacking" of the ubiquitin-proteasome system using proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic...
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.
Topics: Proteolysis; Ubiquitin-Protein Ligases; Nuclear Proteins; Transcription Factors; Ubiquitination
PubMed: 37443112
DOI: 10.1038/s41467-023-39904-5 -
Molecules (Basel, Switzerland) May 2023A potential therapeutic strategy to treat conditions brought on by the aberrant production of a disease-causing protein is emerging for targeted protein breakdown using... (Review)
Review
A potential therapeutic strategy to treat conditions brought on by the aberrant production of a disease-causing protein is emerging for targeted protein breakdown using the PROTACs technology. Few medications now in use are tiny, component-based and utilize occupancy-driven pharmacology (MOA), which inhibits protein function for a short period of time to temporarily alter it. By utilizing an event-driven MOA, the proteolysis-targeting chimeras (PROTACs) technology introduces a revolutionary tactic. Small-molecule-based heterobifunctional PROTACs hijack the ubiquitin-proteasome system to trigger the degradation of the target protein. The main challenge PROTAC's development facing now is to find potent, tissue- and cell-specific PROTAC compounds with favorable drug-likeness and standard safety measures. The ways to increase the efficacy and selectivity of PROTACs are the main focus of this review. In this review, we have highlighted the most important discoveries related to the degradation of proteins by PROTACs, new targeted approaches to boost proteolysis' effectiveness and development, and promising future directions in medicine.
Topics: Proteolysis; Proteasome Endopeptidase Complex; Cytoplasm; Head; Medicine; Proteolysis Targeting Chimera
PubMed: 37241755
DOI: 10.3390/molecules28104014 -
Angewandte Chemie (International Ed. in... Jan 2024Proteolysis targeting chimera (PROTAC) is a state-of-the-art technology for ablating undruggable targets. A PROTAC degrader achieves targeted protein degradation (TPD)... (Review)
Review
Proteolysis targeting chimera (PROTAC) is a state-of-the-art technology for ablating undruggable targets. A PROTAC degrader achieves targeted protein degradation (TPD) through the simultaneous binding of a protein of interest (POI) and an E3 ligase to form a ternary complex. A nanofibril-based PROTAC strategy to form a polynary (E3) : PROTAC : (POI) complex has not been reported in the TPD field up to this point. A recent innovation shows that a POI ligand and E3 ligase ligand don't have to be within a fused degrader molecule. Instead, they can be recruited to cellular proximity by a self-assembly-driving peptide and click chemistry. The resulting nanofibrils can recruit multiple POI and E3 ligase molecules to form a polynary complex as a degradation center. The so-called Nano-PROTAC provides a novel approach for TPD in cancer therapy.
Topics: Proteolysis; Ligands; Ubiquitin-Protein Ligases; Peptides
PubMed: 38059785
DOI: 10.1002/anie.202316581 -
The Journal of Physical Chemistry. B Jul 2020The proteasome is a key protease in the eukaryotic cells which is responsible for various important cellular processes such as the control of the cell cycle, immune...
The proteasome is a key protease in the eukaryotic cells which is responsible for various important cellular processes such as the control of the cell cycle, immune responses, protein homeostasis, inflammation, apoptosis, and the response to proteotoxic stress. Acting as a major molecular machine for protein degradation, proteasome first identifies damaged or obsolete regulatory proteins by attaching ubiquitin chains and subsequently utilizes conserved pore loops of the heterohexameric ring of AAA+ (ATPases associated with diverse cellular activities) to pull and mechanically unfold and translocate the misfolded protein to the active site for proteolysis. A detailed knowledge of the reaction mechanism for this proteasomal proteolysis is of central importance, both for fundamental understanding and for drug discovery. The present study investigates the mechanism of the proteolysis by the proteasome with full consideration of the protein's flexibility and its impact on the reaction free energy. Major attention is paid to the role of the protein electrostatics in determining the activation barriers. The reaction mechanism is studied by considering a small artificial fluorogenic peptide substrate (Suc-LLVY-AMC) and evaluating the activation barriers and reaction free energies for the acylation and deacylation steps, by using the empirical valence bond method. Our results shed light on the proteolysis mechanism and thus should be important for further studies of the proteasome action.
Topics: Adenosine Triphosphatases; Cytoplasm; Proteasome Endopeptidase Complex; Proteolysis; Ubiquitin
PubMed: 32498514
DOI: 10.1021/acs.jpcb.0c04435 -
Journal of Medicinal Chemistry Jul 2023Within druggable target space, new small-molecule modalities, particularly covalent inhibitors and targeted degraders, have expanded the repertoire of medicinal... (Review)
Review
Within druggable target space, new small-molecule modalities, particularly covalent inhibitors and targeted degraders, have expanded the repertoire of medicinal chemists. Molecules with such modes of action have a large potential not only as drugs but also as chemical probes. Criteria have previously been established to describe the potency, selectivity, and properties of small-molecule probes that are qualified to enable the interrogation and validation of drug targets. These definitions have been tailored to reversibly acting modulators but fall short in their applicability to other modalities. While initial guidelines have been proposed, we delineate here a full set of criteria for the characterization of covalent, irreversible inhibitors as well as heterobifunctional degraders ("proteolysis-targeting chimeras", or PROTACs) and molecular glue degraders. We propose modified potency and selectivity criteria compared to those for reversible inhibitors. We discuss their relevance and highlight examples of suitable probe and pathfinder compounds.
Topics: Proteolysis; Ubiquitin-Protein Ligases
PubMed: 37403870
DOI: 10.1021/acs.jmedchem.3c00550 -
Trends in Pharmacological Sciences May 2023Anticancer-targeted therapies inhibit various kinases implicated in cancer and have been used in clinical settings for decades. However, many cancer-related targets are... (Review)
Review
Anticancer-targeted therapies inhibit various kinases implicated in cancer and have been used in clinical settings for decades. However, many cancer-related targets are proteins without catalytic activity and are difficult to target using traditional occupancy-driven inhibitors. Targeted protein degradation (TPD) is an emerging therapeutic modality that has expanded the druggable proteome for cancer treatment. With the entry of new-generation immunomodulatory drugs (IMiDs), selective estrogen receptor degraders (SERDs), and proteolysis-targeting chimera (PROTAC) drugs into clinical trials, the field of TPD has seen explosive growth in the past 10 years. Several challenges remain that need to be tackled to increase successful clinical translation of TPD drugs. We present an overview of the global landscape of clinical trials of TPD drugs over the past decade and summarize the clinical profiles of new-generation TPD drugs. In addition, we highlight the challenges and opportunities for the development of effective TPD drugs for future successful clinical translation.
Topics: Humans; Proteolysis; Neoplasms; Drug Delivery Systems; Proteolysis Targeting Chimera
PubMed: 37059054
DOI: 10.1016/j.tips.2023.03.003