Heterobifunctional degraders, a class of targeted protein degraders (TPDs), often occupy beyond-rule-of-five (bRo5) chemical space, where traditional passive permeability models─calibrated on drug-like molecules or peptides and based on topological descriptors─have limited applicability. This study explores the predictive value of three-dimensional (3D) descriptors for modeling passive membrane permeability of heterobifunctional degraders in bRo5 chemical space. These include intramolecular hydrogen bonds (IMHBs), radius of gyration (Rgyr), and 3D polar surface area (3D-PSA) derived from conformational ensembles generated from well-tempered metadynamics (WT-MetaD) in explicit chloroform. These 3D ensembles were further refined and Boltzmann-weighted using ANI-2x neural network potentials to better represent molecular flexibility and solvent-relevant low-energy conformers. Three machine learning regression models─random forest regression (RF), partial least-squares (PLS), and linear support vector machines (LSVM)─were trained and evaluated using two-dimensional (2D), 3D, and combined 2D + 3D molecular descriptor sets. The inclusion of 3D descriptors consistently improved predictive performance across all models, notably in the challenging bRo5 chemical space. In the best-performing case (PLS), cross-validated r2 improved from 0.29 to 0.48 with the addition of 3D features. This highlights the added predictive power of 3D features for modeling passive permeability in the challenging bRo5 chemical space, where 2D descriptors alone underperform. Feature importance analysis identified the 3D descriptor Rgyr as the dominant contributor to passive permeability, with additional contributions from 3D-PSA and intramolecular hydrogen bonds (IMHBs). Specifically, on the same held-out split, the linear relationship between permeability and Rgyr appears stronger than the averaged model results (means over 100 randomized 50/50 splits), underscoring the role of Rgyr as a dominant predictor in this data set while highlighting the consistent gains achieved by incorporating 3D information beyond 2D descriptors. Together, these 3D features reflect molecular compactness, spatial polarity, and internal hydrogen bonding─key determinants of passive permeability. These results highlight the utility of physically meaningful, ensemble-derived 3D descriptors for improving permeability prediction and guiding the rational design of permeable compounds in bRo5 chemical space. The Amber-based molecular dynamics workflow developed in this study is broadly applicable to heterobifunctional degraders, facilitating the evaluation of permeability properties across diverse protein targets and E3 ligases.

Histone deacetylase 6 (HDAC6) modulates inflammatory signaling through both its catalytic domain and its zinc-finger ubiquitin-binding domain, which makes inhibiting HDAC6 a promising anti-inflammator...

Chemically induced protein degradation is a powerful alternative to classical inhibition, but some proteins have deeply masked binding pockets that make the development of degrader molecules difficult...

Proteolysis targeting chimeras (PROTACs) promote the degradation of targets by ensuring the proximity of the E3-ligase and the target, and understanding the structure of PROTACs at the atomic level is...

Immunomodulatory imide drugs (IMiDs), including thalidomide, lenalidomide, and pomalidomide, can be used to induce degradation of a protein of interest that is fused to a short degron motif, which oft...

Pharmacological degradation of receptor-interacting protein kinase 1 (RIPK1) offers a compelling therapeutic strategy to overcome its scaffolding role in tumor resistance and enhance the efficacy of i...

A growing array of lysosome-targeting chimeras (LYTACs) have recently emerged as therapeutic candidates to treat malignancies and other diseases via targeted protein degradation. We established a novel dual lysosome-targeting receptor-dependent protein degradation strategy that leverages the synergistic actions of the C-X-C chemokine receptor 4 (CXCR4) and folate receptor 1 (FOLR1) to degrade extracellular and membrane proteins. Using this strategy, we developed dual-receptor lysosome-targeting chimeras to achieve efficient lysosomal degradation of programmed cell death ligand 1 (PD-L1) and epidermal growth factor receptor (EGFR). The EGFR chimera inhibited the growth of transplanted T790M-mutated drug-resistant EGFR-driven lung cancer tumors by degrading EGFR. This dual-targeting strategy exhibits significantly better protein degradation capabilities compared with single lysosome-targeting chimeras, providing a novel platform for developing drugs targeting cancer.

Deconvolution of the protein targets of hit compounds from phenotypic screens, often conducted in live cells, is critical for understanding mechanism of action and identifying potentially hazardous off-target interactions. While photoaffinity labeling and chemoproteomics are long-established approaches for discovering small-molecule-protein interactions in live cells, there are a relatively small number of photoaffinity labeling strategies that can be applied for chemoproteomic target identification studies. Recently, we reported a novel chemical framework for photoaffinity labeling based on the photo-Brook rearrangement of acyl silanes and demonstrated its ability, when appended to protein-targeting ligands, to label recombinant proteins. Here, we report the application of these probes to live cell photoaffinity workflows, demonstrate their complementarity to current state-of-the-art minimalist diazirine-based photoaffinity probes, and introduce a modular synthetic route to access acyl silane scaffolds with improved labeling properties.

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Antibody-based therapeutics encompass diverse modalities for targeting tumor cells. Among these, antibody–drug conjugates (ADCs) and extracellular targeted protein degradation (eTPD) specifically depe...

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Proteolysis-targeting chimeras (PROTACs) have transformed therapeutic interventions by hijacking the ubiquitin–proteasome system. However, their broad application is hindered by inadequate cellular permeability and undesired off-tissue effects. Here, we introduce a modular strategy for the in situ synthesis of PROTACs through pathologically activated bioorthogonal catalysis (ABC-PROTAC), enabling targeted protein degradation specifically in cancer cells. This platform integrates biocompatible, glutathione-activated Click-T-Cu(II) complexes with azido- and acetylene-derived, fragmented PROTAC precursors. These components are encapsulated within AS1411 aptamer-conjugated liposomes to enhance cellular uptake and systemic delivery. Once internalized by nucleolin-overexpressing cancer cells, the Click-T-Cu(II) complexes are activated to catalyze the intracellular assembly of functional PROTACs via click chemistry. This delivery paradigm facilitates efficient degradation of oncoproteins both in vitro and in vivo, resulting in robust antitumor activity with favorable biocompatibility and high selectivity. The modularity of the ABC-PROTAC strategy is demonstrated by utilizing diverse warheads, including small molecules and DNA motifs, to degrade BRD4, PARP1, and NF-κB. Together, this strategy establishes a precise method for targeted protein degradation while minimizing the systemic toxicity associated with conventional PROTACs.

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PROTACs induce degradation by bridging a target protein and E3 ubiquitin ligase. Here, authors show that protein interface frustration correlates with cooperativity, offering a structural metric to pr...

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