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Updated: Sep 18, 2025

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DeepPSA: A Geometric Deep Learning Model for PROTAC Synthetic Accessibility Prediction.

Ran Zhang1, Shihang Wang1, Lin Wang1,2

  • 1Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.

Journal of Chemical Information and Modeling
|June 25, 2025
PubMed
Summary
This summary is machine-generated.

We developed DeepPSA, a deep learning model to predict the synthetic accessibility of Proteolysis-targeting chimeras (PROTACs). This tool aids in designing novel drug candidates by assessing PROTAC synthesis feasibility.

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Area of Science:

  • Drug discovery and design
  • Computational chemistry
  • Artificial intelligence in medicine

Background:

  • Proteolysis-targeting chimeras (PROTACs) are novel therapeutics that induce target protein degradation.
  • PROTAC synthesis is complex, hindering drug development.
  • Existing AI models lack tools for evaluating PROTAC synthetic accessibility.

Purpose of the Study:

  • To develop a computational model for predicting PROTAC synthetic accessibility.
  • To provide a data-driven tool for assessing PROTAC synthesis feasibility.
  • To aid in the design and screening of novel PROTAC compounds.

Main Methods:

  • Developed DeepPSA, a graph-based model using a graph neural network architecture.
  • Trained the model on an in-house dataset of 3644 PROTACs with experimental synthetic data.
  • Evaluated model performance using prediction accuracy and AUROC on test and partitioned datasets.

Main Results:

  • DeepPSA achieved 92.9% prediction accuracy and an AUROC of 0.963 on the test set.
  • The model demonstrated superior performance and generalization ability on structure-based partitioned datasets.
  • DeepPSA is the first model specifically focused on PROTAC synthetic accessibility.

Conclusions:

  • DeepPSA offers a reliable and systematic approach to assess PROTAC synthetic accessibility.
  • The model facilitates efficient design and screening of novel PROTACs.
  • DeepPSA is accessible via a web server and GitHub repository for broader use.