Integrating molecular generation and fingerprints transferring for single-molecule theranostics targeting endoplasmic...

Precise diagnosis and treatment of diseases necessitate quantitative visualization and modulation of subcellular structures. The endoplasmic reticulum (ER), as one of the most essential organelles, presents a complex target due to its intricate morphology and diverse cellular roles. Regulating ER stress offers a promising strategy for treating diseases such as tumors. However, achieving accurate targeting and therapeutic intervention at the subcellular level remains a significant challenge. Thus, there is an urgent need for theranostic agents that can precisely target and modulate ER stress.

This study proposes a novel AI-driven dual-targeting strategy combining "passive + active" mechanisms to efficiently design molecules that resolve the balance between passive ER enrichment and precise modulation. We aim to design multifunctional theranostic molecules that precisely target Grp78, a key biomarker of ER stress, at the atomic level, enabling concurrent imaging and modulation of ER stress.

A machine learning (ML)-based molecular fingerprints transfer method was developed for passive targeting based on identified subcellular targeting substructures. Meanwhile, a deep learning (DL)-based 3D molecular generation model, PM-1, was designed for active targeting through specific receptor interactions. By transferring key fingerprints and fluorescent motifs into PM-1-generated molecules, desired theranostic agents were produced. Their key properties were validated via dynamic simulations and quantitative calculations, followed by wet experiments.

Guided by these strategies, we identified unreported ER-targeting rules by discovering key passive-targeting fingerprints derived from ML models, and generated diverse new structures with high affinity binding to Grp78. We successfully synthesized ABT-CN2, a multidimensional fluorescent agent that demonstrates cost-effective chemical structure (molecular weight <400), robust targeting capability (Pearson's correlation coefficient = 0.93), and potential antitumor activity (IC₅₀ = 53.21 μM).

This work presents a new paradigm for the intelligent design of fluorescent molecular probes with precise organelle-targeting capabilities for integrated diagnosis and therapy.