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The Journal of Physical Chemistry. B Jan 2023Proteolysis targeting chimera (PROTAC) is a novel drug modality that facilitates the degradation of a target protein by inducing proximity with an E3 ligase. In this...
Proteolysis targeting chimera (PROTAC) is a novel drug modality that facilitates the degradation of a target protein by inducing proximity with an E3 ligase. In this work, we present a new computational framework to model the cooperativity between PROTAC-E3 binding and PROTAC-target binding principally through protein-protein interactions (PPIs) induced by the PROTAC. Due to the scarcity and low resolution of experimental measurements, the physical and chemical drivers of these non-native PPIs remain to be elucidated. We develop a coarse-grained (CG) approach to model interactions in the target-PROTAC-E3 complexes, which enables converged thermodynamic estimations using alchemical free energy calculation methods despite an unconventional scale of perturbations. With minimal parametrization, we successfully capture fundamental principles of cooperativity, including the optimality of intermediate PROTAC linker lengths that originates from configurational entropy. We qualitatively characterize the dependency of cooperativity on PROTAC linker lengths and protein charges and shapes. Minimal inclusion of sequence- and conformation-specific features in our current force field, however, limits quantitative modeling to reproduce experimental measurements, but further development of the CG model may allow for efficient computational screening to optimize PROTAC cooperativity.
Topics: Proteolysis; Ubiquitin-Protein Ligases; Proteins; Thermodynamics
PubMed: 36607139
DOI: 10.1021/acs.jpcb.2c05795 -
Cells Feb 2022The Golgi apparatus is a central hub for cellular protein trafficking and signaling. Golgi structure and function is tightly coupled and undergoes dynamic changes in... (Review)
Review
The Golgi apparatus is a central hub for cellular protein trafficking and signaling. Golgi structure and function is tightly coupled and undergoes dynamic changes in health and disease. A crucial requirement for maintaining Golgi homeostasis is the ability of the Golgi to target aberrant, misfolded, or otherwise unwanted proteins to degradation. Recent studies have revealed that the Golgi apparatus may degrade such proteins through autophagy, retrograde trafficking to the ER for ER-associated degradation (ERAD), and locally, through Golgi apparatus-related degradation (GARD). Here, we review recent discoveries in these mechanisms, highlighting the role of the Golgi in maintaining cellular homeostasis.
Topics: Golgi Apparatus; Homeostasis; Membrane Proteins; Protein Transport; Proteolysis
PubMed: 35269404
DOI: 10.3390/cells11050780 -
Molecular Plant Sep 2015Plants as sessile organisms are continuously exposed to abiotic stress conditions that impose numerous detrimental effects and cause tremendous loss of yield. Abiotic... (Review)
Review
Plants as sessile organisms are continuously exposed to abiotic stress conditions that impose numerous detrimental effects and cause tremendous loss of yield. Abiotic stresses, including high sunlight, confer serious damage on the photosynthetic machinery of plants. Photosystem II (PSII) is one of the most susceptible components of the photosynthetic machinery that bears the brunt of abiotic stress. In addition to the generation of reactive oxygen species (ROS) by abiotic stress, ROS can also result from the absorption of excessive sunlight by the light-harvesting complex. ROS can damage the photosynthetic apparatus, particularly PSII, resulting in photoinhibition due to an imbalance in the photosynthetic redox signaling pathways and the inhibition of PSII repair. Designing plants with improved abiotic stress tolerance will require a comprehensive understanding of ROS signaling and the regulatory functions of various components, including protein kinases, transcription factors, and phytohormones, in the responses of photosynthetic machinery to abiotic stress. Bioenergetics approaches, such as chlorophyll a transient kinetics analysis, have facilitated our understanding of plant vitality and the assessment of PSII efficiency under adverse environmental conditions. This review discusses the current understanding and indicates potential areas of further studies on the regulation of the photosynthetic machinery under abiotic stress.
Topics: Light; Photosynthesis; Photosystem II Protein Complex; Proteolysis; Reactive Oxygen Species; Stress, Physiological
PubMed: 25997389
DOI: 10.1016/j.molp.2015.05.005 -
Cold Spring Harbor Perspectives in... Jan 2014When ubiquitin (Ub) is attached to membrane proteins on the plasma membrane, it directs them through a series of sorting steps that culminate in their delivery to the... (Review)
Review
When ubiquitin (Ub) is attached to membrane proteins on the plasma membrane, it directs them through a series of sorting steps that culminate in their delivery to the lumen of the lysosome where they undergo complete proteolysis. Ubiquitin is recognized by a series of complexes that operate at a number of vesicle transport steps. Ubiquitin serves as a sorting signal for internalization at the plasma membrane and is the major signal for incorporation into intraluminal vesicles of multivesicular late endosomes. The sorting machineries that catalyze these steps can bind Ub via a variety of Ub-binding domains. At the same time, many of these complexes are themselves ubiquitinated, thus providing a plethora of potential mechanisms to regulate their activity. Here we provide an overview of how membrane proteins are selected for ubiquitination and deubiquitination within the endocytic pathway and how that ubiquitin signal is interpreted by endocytic sorting machineries.
Topics: Binding Sites; Cell Membrane; Endocytosis; Protein Transport; Proteolysis; Ubiquitin
PubMed: 24384571
DOI: 10.1101/cshperspect.a016808 -
Journal of Dairy Science Mar 2017Strachitunt, a blue-veined Italian cheese, received the Protected Designation of Origin (PDO) label in 2014. Its unique technological feature is represented by the...
Strachitunt, a blue-veined Italian cheese, received the Protected Designation of Origin (PDO) label in 2014. Its unique technological feature is represented by the dual-curd method of production. Strachitunt is produced from raw bovine milk with or without the inoculation of natural starter cultures of lactic acid bacteria, and the addition of secondary cultures of mold spores is not permitted by the product specification. Physico-chemical properties, proteolysis, and volatile profile of Strachitunt were investigated in 10 cheese samples (ripened for 75 d) made throughout spring 2015 and provided by the main cheese maker. Overall, composition parameters showed a large variability among samples. Cheese was characterized by an acid paste (pH 5.46) and a lower extent of proteolysis compared with other blue-veined varieties. The main chemical groups of volatile organic compounds were alcohols and esters, whereas ketones represented only a minor component. The erratic adventitious contamination by mold spores of the cheese milk, the unique dual-curd method of cheese-making, and the large time variability between the piercing time and the end of ripening could be highlighted as the main causes of both the distinctive analytical fingerprint and the scarce standardization of this blue-veined cheese.
Topics: Animals; Cattle; Cheese; Food Handling; Ketones; Milk; Proteolysis; Volatile Organic Compounds
PubMed: 28041724
DOI: 10.3168/jds.2016-11781 -
Current Opinion in Chemical Biology Aug 2017Small molecule probes of biological systems have traditionally been designed to bind to and inhibit the active sites of their protein targets. While this class of... (Review)
Review
Small molecule probes of biological systems have traditionally been designed to bind to and inhibit the active sites of their protein targets. While this class of pharmacological agents has been broadened by the development of a small number of allosteric and protein-protein interaction (PPI) inhibitors, conventional drug design still excludes 'undruggable' proteins that are neither enzymes nor receptors. Recent years have seen the emergence of new classes of small molecules that can target hitherto undruggable proteins by recruiting the cellular proteostasis machinery to selectively tag them for degradation. These molecules, especially the class known as Proteolysis Targeting Chimera (PROTACs), represent a paradigm shift in chemical genetics, but their most tantalizing potential is as novel therapeutic agents. This review briefly summarizes the preclinical development of small molecule-based protein degraders, and describes the recent improvements in the technology that have positioned PROTACs on the cusp of entering the clinic.
Topics: Amino Acid Sequence; Animals; Humans; Proteins; Proteolysis; Small Molecule Libraries
PubMed: 28605671
DOI: 10.1016/j.cbpa.2017.05.016 -
Current Opinion in Pharmacology Aug 2021The field of targeted protein degradation encompasses a growing number of modalities that achieve potent and selective knockdown of target proteins at the... (Review)
Review
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.
Topics: Humans; Proteins; Proteolysis
PubMed: 34058637
DOI: 10.1016/j.coph.2021.04.009 -
Journal of Medicinal Chemistry Mar 2021Bromodomain and extraterminal (BET) proteins bind acetylated lysine residues in histones and nonhistone proteins via tandem bromodomains and regulate chromatin dynamics,... (Review)
Review
Bromodomain and extraterminal (BET) proteins bind acetylated lysine residues in histones and nonhistone proteins via tandem bromodomains and regulate chromatin dynamics, cellular processes, and disease procession. Thus targeting BET proteins is a promising strategy for treating various diseases, especially malignant tumors and chronic inflammation. Many pan-BET small-molecule inhibitors have been described, and some of them are in clinical evaluation. Nevertheless, the limited clinical efficacy of the current BET inhibitors is also evident and has inspired the development of new technologies to improve their clinical outcomes and minimize unwanted side effects. In this Review, we summarize the latest protein characteristics and biological functions of BRD4 as an example of BET proteins, analyze the clinical development status and preclinical resistance mechanisms, and discuss recent advances in BRD4-selective inhibitors, dual-target BET inhibitors, proteolysis targeting chimera degraders, and protein-protein interaction inhibitors.
Topics: Amino Acid Sequence; Animals; Cell Line, Tumor; Clinical Trials as Topic; Drug Discovery; Humans; Organic Chemicals; Protein Binding; Protein Domains; Protein Multimerization; Proteolysis; Transcription Factors
PubMed: 33616410
DOI: 10.1021/acs.jmedchem.0c01487 -
Drug Discovery Today. Technologies Apr 2019A new series of therapeutic modalities resulting in degradation of target proteins, termed proteolysis targeting chimeras (PROTACs), hold significant therapeutic... (Review)
Review
A new series of therapeutic modalities resulting in degradation of target proteins, termed proteolysis targeting chimeras (PROTACs), hold significant therapeutic potential with possible prolonged pharmacodynamics, improved potency, and ability to target proteins previously thought of as "undruggable". PROTACs are heterobifunctional small molecules consisting of a target binding handle bridged via a chemical linker to an E3 ligase handle which recruit the E3 ligase and ubiquitin machinery to target proteins, resulting in subsequent ubiquitination and degradation of the target. With the generation of small molecule PROTAC compound libraries for drug discovery, it becomes essential to have sensitive screening technologies to rapidly profile activity and have assays which can clearly inform on performance at the various cellular steps required for PROTAC-mediated degradation. For PROTAC compounds, this has been particularly challenging using either biochemical or cellular assay approaches. Biochemical assays are highly informative for the first part of the degradation process, including optimization of compound binding to targets and interrogation of target:PROTAC:E3 ligase ternary complex formation, but struggle with the remaining steps; recruitment of ternary complex into larger active E3 ligase complexes, ubiquitination, and proteasomal degradation. On the other hand, cellular assays are excellent at determining if the PROTAC successfully degrades the target in its relevant setting but struggle as early development PROTAC compounds are often poorly cell-permeable given their high molecular weight. Additionally, if degradation is not observed in a cellular assay, it is difficult to deconvolute the reason why or at which step there was failure. In this review we will highlight the current approaches along with recent advances to overcome the challenges faced for cellular PROTAC screening, which will enable and advance drug discovery of therapeutic degradation compounds.
Topics: Drug Discovery; Proteins; Proteolysis
PubMed: 31200861
DOI: 10.1016/j.ddtec.2018.12.001 -
Journal of Medicinal Chemistry Jul 2022Proteolysis targeting chimera (PROTAC)-mediated protein degradation has prompted a radical rethink and is at a crucial stage in driving a drug discovery transition. To... (Review)
Review
Proteolysis targeting chimera (PROTAC)-mediated protein degradation has prompted a radical rethink and is at a crucial stage in driving a drug discovery transition. To fully harness the potential of this technology, a growing paradigm toward enriching PROTACs with other therapeutic modalities has been proposed. Could researchers successfully combine two modalities to yield PROTACs with an expanded profile? In this Perspective, we try to answer this question. We discuss how this possibility encompasses different approaches, leading to PROTACs, PROTACs, PROTAC , and and PROTACs. This possibility promises to further enhance PROTAC efficacy and selectivity, minimize side effects, and hit undruggable targets. While PROTACs have reached the clinical investigation stage, additional steps must be taken toward the translational development of PROTACs. A deeper and detailed understanding of the most critical challenges is required to fully exploit these opportunities and decisively enrich the PROTAC toolbox.
Topics: Drug Discovery; Proteolysis; Ubiquitin-Protein Ligases
PubMed: 35816671
DOI: 10.1021/acs.jmedchem.2c00302