AIMC Topic: Ubiquitin-Protein Ligases
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SE(3)-equivariant ternary complex prediction towards target protein degradation.
Nature communications
Jul 1, 2025
Targeted protein degradation (TPD) has rapidly emerged as a powerful modality for drugging previously "undruggable" proteins. TPD employs small molecules like PROTACs and molecular glue degraders (MGD) to induce target protein degradation via the for...
Therapeutic potential of allosteric HECT E3 ligase inhibition.
Cell
Apr 2, 2025
Targeting ubiquitin E3 ligases is therapeutically attractive; however, the absence of an active-site pocket impedes computational approaches for identifying inhibitors. In a large, unbiased biochemical screen, we discover inhibitors that bind a crypt...
An artificial intelligence accelerated virtual screening platform for drug discovery.
Nature communications
Sep 5, 2024
Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries. However, the success of virtual screening crucially depends on the accuracy of the binding p...
Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells.
Science (New York, N.Y.)
Apr 26, 2024
Chemical modulation of proteins enables a mechanistic understanding of biology and represents the foundation of most therapeutics. However, despite decades of research, 80% of the human proteome lacks functional ligands. Chemical proteomics has advan...
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs.
Journal of chemical information and modeling
Mar 19, 2024
Proteolysis-targeting chimeras (PROTACs) that engage two biological targets at once are a promising technology in degrading clinically relevant protein targets. Since factors that influence the biological activities of PROTACs are more complex than t...
Discovery of a Novel DCAF1 Ligand Using a Drug-Target Interaction Prediction Model: Generalizing Machine Learning to New Drug Targets.
Journal of chemical information and modeling
Jun 23, 2023
DCAF1 functions as a substrate recruitment subunit for the RING-type CRL4 and the HECT family EDVP E3 ubiquitin ligases. The WDR domain of DCAF1 serves as a binding platform for substrate proteins and is also targeted by HIV and SIV lentiviral adapto...
Bifunctional robots inducing targeted protein degradation.
European journal of medicinal chemistry
Apr 15, 2023
The gaining importance of Targeted Protein Degradation (TPD) and PROTACs (PROteolysis-TArgeting Chimeras) have drawn the scientific community's attention. PROTACs are considered bifunctional robots owing to their avidity for the protein of interest (...
Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence.
Journal of the American Chemical Society
Jan 27, 2023
Only around 20% of the human proteome is considered to be druggable with small-molecule antagonists. This leaves some of the most compelling therapeutic targets outside the reach of ligand discovery. The concept of targeted protein degradation (TPD) ...
DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs.
Nature communications
Nov 21, 2022
The rational design of PROTACs is difficult due to their obscure structure-activity relationship. This study introduces a deep neural network model - DeepPROTACs to help design potent PROTACs molecules. It can predict the degradation capacity of a pr...
Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning.
BMC biology
Jul 14, 2022
BACKGROUND: Degrons are short linear motifs, bound by E3 ubiquitin ligase to target protein substrates to be degraded by the ubiquitin-proteasome system. Mutations leading to deregulation of degron functionality disrupt control of protein abundance d...
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