Molecular mechanisms of skeletal muscle atrophy: clinical challenges and future therapeutic strategies.

New insights into the ambivalent role and clinical implications of tripartite motif family proteins in colorectal cancer.

The ubiquitin-proteasome system is one of the primary mechanisms responsible for degradation of intracellular proteins. Cullin-RING E3 ligases (CRL) are modular, multi-subunit complexes that catalyse ubiquitination of a wide variety of proteins, marking them for degradation by the proteasome. Substrate specificity is conferred by the substrate receptor subunit of the CRL, of which there are hundreds. Targeted protein degradation (TPD) is a drug modality that involves hijacking the activity of CRLs to ubiquitinate non-native neosubstrates via compound-induced ternary complex formation between a substrate receptor and the target. Of the many CRL substrate receptors, the DDB1- and Cul4-associated factor (DCAF) family are of high interest and potential for TPD. To enable characterisation of DCAF proteins and ligand screening campaigns, we have undertaken high-throughput recombinant protein expression screening in insect cells and small-scale plate-based purification of 24 DCAF proteins to identify soluble recombinant protein. Co-expression with the stabilising substrate adaptor DDB1 is required for, or enhances, expression of many DCAFs and provides a folding quality control measure through co-purification with tagged DCAF protein. Of 13 DCAF proteins that had not previously been expressed in the literature, we identify 8 that express well as promising candidates for scale-up. We provide sequence and construct information as a resource for the community. This screening method could be expanded to more DCAF proteins and applied to other CRL substrate receptor families.

Proteolysis Targeting Chimeras (PROTACs) represent a transformative approach to drug development by leveraging the intracellular ubiquitin-proteasome system (UPS) for the selective degradation of target proteins. A PROTAC molecule comprises three essential components: a ligand that binds to the E3 ubiquitin ligase, a ligand that targets the protein of interest, and a flexible linker that connects the two. This distinctive structure enables the PROTAC to simultaneously engage with both the target protein and the E3 ligase, facilitating their interaction. Such proximity initiates the ubiquitination of the target protein, marking it for recognition and subsequent degradation. In this study, we benchmark ternary complexes based on PROTACs using four recently employed predictive tools: Chai-1, AlphaFold2, AlphaFold3, and Protenix. Comparative analysis indicated that the ternary complexes predicted by the four prediction tools demonstrated satisfactory accuracy (Cα-RMSD < 10 Å). Among the evaluated tools, three-Chai-1, AlphaFold3, and Protenix-demonstrated superior performance in over half of the tests, while AlphaFold2 exhibited comparatively lower performance. However, significant challenges remained in accurately predicting the orientation of POI and the E3 ligase (Cα-RMSD < 10 Å when POI or E3 ligase were used as reference), as well as the position of the small molecule PROTAC (RMSD < 5 Å). By benchmarking these tools, we underscore recent advancements in protein structure prediction, enhance our understanding of the mechanisms underpinning PROTAC complexes, and provide a valuable reference for evaluating the binding conformations of other ternary complexes, as well as for the development of future predictive tools.

Predicting PROTAC degradation activity and selectivity of effective E3 ligase through harnessing a combination of AtomPair fingerprints and multiple machine learning algorithms.

CDDO-Me alleviates doxorubicin/lapatinib-induced cardiotoxicity by activating the NRF2/GPX4 axis to inhibit oxidative stress and ferroptosis.

Skeletal Muscle Mass and Quality in Peripheral Artery Disease: New Insights into Clinical Management and Therapeutic Optimization.

Interstitial deletions involving 3q27.1 define a distinct microdeletion syndrome characterized by prenatal-onset growth restriction, postnatal microcephaly, hypotonia, intellectual disability, and distinctive craniofacial features. While AP2M1 haploinsufficiency has been proposed as the primary driver of this phenotype, the full spectrum of dosage-sensitive genes within the locus remains unclear. Here, we report a patient with a de novo heterozygous 3q27.1 microdeletion and delineate a refined minimal smallest region of overlap (SRO) of approximately 189 kb, representing the narrowest critical interval associated with the 3q27.1 microdeletion phenotype to date. Chromosomal microarray and exome-based CNV analysis confirmed the deletion, which encompasses PSMD2, EIF4G1, and POLR2H but excludes AP2M1 and DVL3. The patient exhibited severe intrauterine growth restriction, microcephaly, global developmental delay, and mild dysmorphism, consistent with the established 3q27.1 phenotype. PSMD2 encodes a non-ATPase regulatory subunit of the 26S proteasome, and its loss may disrupt proteasome-mediated protein turnover and neuronal homeostasis. Comparison with previously published cases and an overlapping ClinVar variant (ID: 60129) with similar features supports the pathogenicity of this minimal deletion. Our findings refine the 3q27.1 critical region, propose PSMD2 haploinsufficiency as a likely molecular mechanism underlying growth and neurodevelopmental defects. Further cases and functional studies are needed to confirm PSMD2 causality and clarify the proteasome-related mechanisms underlying 3q27.1 microdeletion syndrome.

The 26S proteasome engages in priming explants with auxin plus cytokinin for somatic embryogenesis of Coffea canephora.

From the arrival of the SARS-CoV-2 coronavirus in 2019 and its associated COVID-19 pandemic, worldwide efforts have been focused on developing a drug to treat patients. The SARS-CoV-2 main protease (Mpro) is one of the main targets for drug design due to its key role in the virus replication and its distinguished ability to cleave peptides after a glutamine residue. Inspired by the knowledge of the inhibition mechanism of 20S Proteasome, this work focuses on exploring the inhibition process of SARS-CoV-2 Mpro with a β-lactone, as well as the impact of the stereochemistry of this compound on the stability of the enzyme:inhibitor binding formation complex. Based on molecular dynamics simulations with classical and hybrid QM/MM potentials, the free energy landscape of the mechanism of the formation of the covalent complex has been computed. The results show how one of the stereoisomers of the β-lactone derivative forms a stable reactant non-covalent complex in the active site of Mpro. Analysis of the kinetics and thermodynamics of the inhibition process suggests that this non-peptidyl compound can be considered a lead compound for future developments of efficient therapeutic compounds to treat patients with COVID-19.

Variants in KLHL15, encoding a regulator of protein ubiquitination, linked to focal epilepsy with neurodevelopmental disorders.

BAG3V468M impairs proteasomal protein clearance and induces dilated cardiomyopathy in vivo.

Targeted protein degradation in inflammatory bone diseases: Mechanistic basis and therapeutic opportunities.

Overcoming breast cancer resistance through targeted protein degradation and next generation chimeras.

Despite the paradigm shift brought about by anti-VEGF therapy against neovascular age-related macular degeneration, significant challenges persist, including the risk of intraocular infection and retinal structural damage caused by frequent intravitreal injections, suboptimal long-term outcomes in some patients, as well as economic and psychological burdens. Attempts to identify novel therapeutic targets with more compliant drug delivery strategies are warranted. In this study, we identify that nucleolin (NCL) is upregulated in choroidal neovascularization lesions and mobilized to the endothelial cell surface upon VEGF stimulation. Inspired by this localization change and the critical role of NCL in angiogenesis, we developed an integrated delivery and degradation platform, named dNCL@tFNAs, which leverages tetrahedral framework nucleic acids (tFNAs) to decorate an aptamer-based proteolysis-targeting chimera for NCL through a simple Watson-Crick pairing. dNCL@tFNAs exhibits notable stability, improved ocular penetration and degradation efficiency. Mechanistic study reveals that membrane-associated NCL promotes the uptake of dNCL@tFNAs into the endothelial cells, followed by engaging the cytosolic PROTAC machinery to degrade intracellular NCL via the ubiquitin-proteasome pathway. In vivo study demonstrates that dNCL@tFNAs enables administration via a minimally invasive subconjunctival injection to suppress choroidal neovascularization with a favorable safety profile. Collectively, our work establishes a programmable delivery and degradation modality for the treatment of choroidal neovascularization and other ocular neovascular diseases.

Ferroptosis, an iron-dependent cell death, is a promising target in gastric cancer. METTL3, an m6A RNA methyltransferase, drives tumor progression, but its role in ferroptosis regulation and the involved deubiquitinating enzymes (DUBs) remain unclear. Here, we demonstrated that METTL3 expression heterogeneity in different gastric cancer cells, identified functional role of METTL3 in modulating ferroptosis sensitivity. In MKN-7 and GCIY cells, forced METTL3 overexpression conferred resistance to ferroptotic stress by driven GPX4 and FTH1 expression, and inhibiting oxidative stress accumulation. Conversely, METTL3 depletion sensitized cells to ferroptosis, and promoted ferroptotic oxidative damage. Through a comprehensive screening of deubiquitinases, we identified ubiquitin specific peptidase 48 (USP48) as a critical stabilizer of METTL3 protein. Functional assays revealed that USP48 mimics METTL3's protective role against ferroptosis, while METTL3 overexpression rescued the ferroptosis sensitivity caused by USP48 knockdown. Mechanistically, this USP48-METTL3 axis regulated key ferroptosis markers including GPX4, FTH1, lipid peroxidation, iron accumulation, and reactive oxygen species (ROS) levels. Our findings reveal a novel regulatory pathway by which USP48 controls ferroptosis sensibility in gastric cancer cell via METTL3 stabilization. This crosstalk between the ubiquitin-proteasome system and m6A transferases highlights the USP48-METTL3 axis as a promising target to sensitize gastric cancer cells to ferroptosis-inducing therapy.

Deletion of Fbxo25 causes excessive repetitive behavior, impaired recognition memory, reduced dendritic complexity, and aberrant protein expression in mice.

Proteolysis-targeting chimeras (PROTAC) are an innovative treatment approach that selectively breaks down disease-relevant proteins by utilizing the ubiquitin-proteasome system. Other than PROTAC, Molecular glue, Lysosome-Targeting Chimaera (LYTAC), GlueTAC, Autophagy-Targeting Chimaera (AUTAC), Autophagosome Tethering Compound (ATTEC), and Antibody-based PROTAC (AbTAC) are emerging targeted protein degradation (TPD) techniques, of which PROTAC offers several benefits. This review discusses the development of proteolysis-targeting chimeras (PROTACs) for targeted protein degradation, highlighting their mechanism of action via the ubiquitin - proteasome system. It examines key physicochemical and pharmacokinetic challenges that limit clinical translation. Advanced formulation strategies, including nanoformulations and amorphous solid dispersions, prodrug improve solubility, bioavailability, and therapeutic efficacy. Additionally, characterization techniques are summarized, and the review outlines recent progress and critical considerations for the successful clinical translation of PROTAC-based therapeutics. Relevant articles from PubMed, Scopus, and Web of Science, spanning publications up to 2026, were gathered. PROTACs represent a transformative therapeutic modality, enabling selective protein degradation beyond conventional inhibition. Future research should focus on improving bioavailability, targeted delivery, and stability, while advancing prodrug strategies, E3 ubiquitin ligase selectivity, oral formulations, and predictive models for clinical translation. Additionally, it should emphasize scalable manufacturing, regulatory frameworks, and integration with emerging targeted protein degradation technologies.

Selective degradation of platelet BTK by PROTAC NX-5948 provides antithrombotic benefits without affecting haemostasis.

Targeted protein degradation (TPD) has emerged as a transformative strategy in drug discovery, yet the repertoire of E3 ligase recruiters remains limited. Here, we report the discovery of an aldehyde-anchored PROTAC that covalently engages the E3 ligase FBXO22 to induce degradation of the histone methyltransferase NSD2 and CDK12. Competitive electrophile screening identified a phenyl aldehyde warhead as optimal, with SAR studies revealing that degradation is highly sensitive to the steric and electronic environment of the aldehyde moiety. The lead degrader, T9, effectively and selectively induces NSD2 degradation across multiple cancer cell lines. Mechanistic investigations confirmed that degradation is dependent on FBXO22, the ubiquitin-proteasome system, and the neddylation pathway, with mutagenesis identifying Cys326 as the critical residue for covalent engagement. This work establishes a stable covalent ligand for FBXO22, expanding chemical space of PROTAC design by introducing an accessible aldehyde-based E3 ligase ligand with broad potential for protein degradation.