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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 -
Chembiochem : a European Journal of... Dec 2023Small molecules inducing protein degradation are important pharmacological tools to interrogate complex biology and are rapidly translating into clinical agents....
Small molecules inducing protein degradation are important pharmacological tools to interrogate complex biology and are rapidly translating into clinical agents. However, to fully realise the potential of these molecules, selectivity remains a limiting challenge. Herein, we addressed the issue of selectivity in the design of CRL4 recruiting PROteolysis TArgeting Chimeras (PROTACs). Thalidomide derivatives used to generate CRL4 recruiting PROTACs have well described intrinsic monovalent degradation profiles by inducing the recruitment of neo-substrates, such as GSPT1, Ikaros and Aiolos. We leveraged structural insights from known CRL4 neo-substrates to attenuate and indeed remove this monovalent degradation function in well-known CRL4 molecular glues degraders, namely CC-885 and Pomalidomide. We then applied these design principles on a previously published BRD9 PROTAC (dBRD9-A) and generated an analogue with improved selectivity profile. Finally, we implemented a computational modelling pipeline to show that our degron blocking design does not impact PROTAC-induced ternary complex formation. We believe that the tools and principles presented in this work will be valuable to support the development of targeted protein degradation.
Topics: Ubiquitin-Protein Ligases; Proteolysis
PubMed: 37418539
DOI: 10.1002/cbic.202300351 -
Ultrasonics Sonochemistry Oct 2020Ultrasound (US) is an emerging technology capable of affecting enzymes and microorganisms, leading to the release of amino acids and the formation of volatile compounds....
Ultrasound (US) is an emerging technology capable of affecting enzymes and microorganisms, leading to the release of amino acids and the formation of volatile compounds. The effect of different exposure times (0, 3, 6, and 9 min) of US (25 kHz, 128 W) on the proteolysis and volatile compounds of dry fermented sausages during processing (day 0 and 28) and storage (day 1 and 120) was investigated. Lower alanine, glycine, valine, leucine, proline, methionine, and tyrosine levels were observed at the beginning of manufacture for the sample subjected to 9 min of US (p < 0.05) when compared to the control. During the storage period, the samples subjected to US exposure for 3 and 6 min exhibited higher free amino acid levels. A greater formation of hexanal, pentanal, and hexanol was observed in the US-treated samples when compared to the control (p < 0.05), as well as other derivatives from the oxidation reactions during the storage. The use of US (25 kHz and 128 W) in the manufacture of dry fermented sausages can affect the proteolysis and the formation of compounds derived from lipid oxidation during the storage.
Topics: Fermentation; Meat Products; Proteolysis; Sonication; Volatile Organic Compounds
PubMed: 32388311
DOI: 10.1016/j.ultsonch.2020.105161 -
European Journal of Medicinal Chemistry Nov 2023Targeted protein degradation (TPD) has emerged as a promising approach for drug development, particularly for undruggable targets. TPD technology has also been... (Review)
Review
Targeted protein degradation (TPD) has emerged as a promising approach for drug development, particularly for undruggable targets. TPD technology has also been instrumental in overcoming drug resistance. While some TPD molecules utilizing proteolysis-targeting chimera (PROTACs) or molecular glue strategies have been approved or evaluated in clinical trials, hydrophobic tag-based protein degradation (HyT-PD) has also gained significant attention as a tool for medicinal chemists. The increasing number of reported HyT-PD molecules possessing high efficiency in degrading protein and good pharmacokinetic (PK) properties, has further fueled interest in this approach. This review aims to present the design rationale, hydrophobic tags in use, and diverse mechanisms of action of HyT-PD. Additionally, the advantages and disadvantages of HyT-PD in protein degradation are discussed. This review may help inspire the development of more HyT-PDs with superior drug-like properties for clinical evaluation.
Topics: Humans; Proteolysis; Drug Development; Proteolysis Targeting Chimera; Skin Neoplasms; Technology
PubMed: 37607438
DOI: 10.1016/j.ejmech.2023.115741 -
Nature Chemical Biology Oct 2019Targeted protein degradation as a therapeutic modality has seen dramatic progress and massive investment in recent years because of the convergence of two key scientific... (Review)
Review
Targeted protein degradation as a therapeutic modality has seen dramatic progress and massive investment in recent years because of the convergence of two key scientific breakthroughs: optimization of first-generation peptidic proteolysis-targeted chimeras (PROTACs) into more drug-like molecules able to support in vivo proof of concept and the discovery that clinical molecules function as degraders by binding and repurposing the proteins cereblon and DCAF15. This provided clinical validation for the general approach through the cereblon modulator class of drugs and provided highly drug-like and ligand-efficient E3 ligase binders upon which to tether target-binding moieties. Increasingly rational and systematic approaches including biophysical and structural studies on ternary complexes are being leveraged as the field advances. In this Perspective we summarize the discoveries that have laid the foundation for future degradation therapeutics, focusing on those classes of small molecules that redirect E3 ubiquitin ligases to non-native substrates.
Topics: Binding Sites; Humans; Proteasome Endopeptidase Complex; Protein Binding; Proteolysis; Small Molecule Libraries; Ubiquitin-Protein Ligases
PubMed: 31527835
DOI: 10.1038/s41589-019-0362-y -
Biophysical Journal Feb 2018
Topics: Biological Assay; Collagen; Mechanical Phenomena; Physical Phenomena; Proteolysis
PubMed: 29414694
DOI: 10.1016/j.bpj.2017.11.3788 -
Analytical Chemistry Feb 2021Sensitive and facile detection of biomarkers is essential for early diagnosis and treatment of diseases. To this end, we here proposed a colorimetric protease assay by...
Sensitive and facile detection of biomarkers is essential for early diagnosis and treatment of diseases. To this end, we here proposed a colorimetric protease assay by the modular combination of proteolysis-responsive transcription and spherical nucleic acids (SNAs). In this assay, target protease-mediated proteolysis triggers the synthesis of RNAs by transcription, which subsequently results in the aggregation of SNAs with remarkable redshifts in the wavelength of surface plasmon resonance-related absorption. As a proof of concept, this assay achieved the sensitive and specific detection of matrix metalloprotease-2 (MMP-2) with a limit of detection of 3.3 pM. Moreover, the applicability of this colorimetric assay can be expanded to other protease biomarkers (e.g., thrombin and hepatitis C virus NS3/4A) by tuning the target-responsive RNA polymerase module. Furthermore, by the immobilization of SNAs on a glass fiber membrane, a test strip that enables the portable detection of target protease with a smartphone was developed. With the use of a mobile application to capture and process the colorimetric signals, this portable detection system allowed for sensitive evaluation of MMP-2 levels in biological and clinical specimens, highlighting its potential in point-of-care diagnosis of diseases.
Topics: Biomarkers; Colorimetry; Nucleic Acids; Peptide Hydrolases; Proteolysis; Smartphone
PubMed: 33544577
DOI: 10.1021/acs.analchem.0c04894 -
ACS Nano Apr 2020Bioorthogonal activation of prodrugs provides a strategy for on-demand on-site production of therapeutics. Intracellular activation provides a strategy to localize...
Bioorthogonal activation of prodrugs provides a strategy for on-demand on-site production of therapeutics. Intracellular activation provides a strategy to localize therapeutics, potentially minimizing off-target effects. To this end, nanoparticles embedded with transition metal catalysts (nanozymes) were engineered to generate either "hard" irreversible or "soft" reversible coronas in serum. The hard corona induced nanozyme aggregation, effectively inhibiting nanozyme activity, whereas only modest loss of activity was observed with the nonaggregating soft corona nanozymes. In both cases complete activity was restored by treatment with proteases. Intracellular activity mirrored this reactivation: endogenous proteases in the endosome provided intracellular activation of both nanozymes. The role of intracellular proteases in nanozyme reactivation was verified through treatment of the cells with protease inhibitors, which prevented reactivation. This study demonstrates the use of intracellular proteolysis as a strategy for localization of therapeutic generation to within cells.
Topics: Catalysis; Endosomes; Protein Corona; Proteolysis; Transition Elements
PubMed: 32227914
DOI: 10.1021/acsnano.0c00629 -
Biosensors & Bioelectronics Sep 2021Various types of molecules serve as biomarkers of diseases, and numerous methods have been reported to detect and quantify them. Recently, research efforts have been...
Various types of molecules serve as biomarkers of diseases, and numerous methods have been reported to detect and quantify them. Recently, research efforts have been made to develop point-of-care (POC) tests, which contribute to early diagnoses of diseases, particularly in resource-limited settings. An assay performed in a homogeneous phase is an obvious route to develop these methods. Here, simple homogeneous methods based on proximity proteolysis reactions (PPR) are reported to detect biological molecules. A typical PPR system has been designed such that the proteolysis reaction between protease and zymogen is enhanced in the presence of a target analyte. The activated zymogen generates a color signal by hydrolyzing a chromophore. A protease and zymogen are linked to target binders using specific hybridization between complementary single-stranded DNAs, and several molecules, including proteins, antibodies, aptamers, and small molecules, are used as target binders. The developed assay methods successfully detected several kinds of analytes at subnanomolar concentrations with the one-step procedure and color signal. The modular design of the PPR-based assay will enable the development of simple POC diagnostics for various biomarkers.
Topics: Biosensing Techniques; Colorimetry; DNA, Single-Stranded; Nucleic Acid Hybridization; Proteolysis
PubMed: 34030090
DOI: 10.1016/j.bios.2021.113349 -
Bioorganic Chemistry Oct 2023The technology known asPROTACs (PROteolysisTArgeting Chimeras) is a method of protein degradation. Utilising bifunctional small molecules, the ubiquitin-proteosome... (Review)
Review
The technology known asPROTACs (PROteolysisTArgeting Chimeras) is a method of protein degradation. Utilising bifunctional small molecules, the ubiquitin-proteosome system (UPS) is used to induce the ubiquitination and degradation of target proteins. In addition to being novel chemical knockdown agents for biological studies that are catalytic, reversible, and rapid, PROTACs used in the treatment for disorders like cancer, immunological disorders, viral diseases, and neurological disorders. The protein degradation field has advanced quickly over the last two years, with a significant rise in research articles on the subject as well as a quick rise in smallmolecule degraders that are currently in or will soon enter the clinical stage. Other new degrading technologies, in addition to PROTAC and molecular glue technology, are also emerging rapidly. In this review article, we mainly focuses on various PROTAC molecules designed with special emphasis on targeted cellular pathways for different diseases i.e., cancer, Viral diseases Immune disorders, Neurodegenerative diseases, etc. We discussed about new technologies based on PROTACs such as Antibody PROTAC, Aptamers, Dual target, Folate caged, TF PROTAC, etc. Also, we listed out the PROTACs which are in clinical trials.
Topics: Proteolysis; Proteolysis Targeting Chimera; Proteasome Endopeptidase Complex; Antibodies; Catalysis
PubMed: 37480814
DOI: 10.1016/j.bioorg.2023.106720