RetroMPA: A MolecularProperty-Aware Auxiliary Frameworkfor Enhancing Retrosynthesis Prediction

Abstract Retrosynthesis is a cornerstone of drug discovery and organic synthesis. While data-driven deep learning models have shown remarkable progress, they are designed to autonomously learn reaction patterns from extensive retrosynthesis data sets with limited explicit integration of established chemical knowledge as priors. To address this limitation, we introduce RetroMPA, a molecular property-aware, posthoc enhancement module that injects chemical knowledge into the retrosynthesis pipeline. Rather than functioning as an independent, standalone SMILES sequence generator from scratch, RetroMPA is conceptualized as a broadly applicable, model-agnostic chemical filter designed to recalibrate and optimize the predictive pathways of various existing algorithms. This plug-and-play framework can be seamlessly integrated with a range of existing data-driven retrosynthesis methods, enhancing model outputs without necessitating any modifications to the original model architecture or requiring resource-intensive, model-specific retraining procedures. By operating at the molecular level and leveraging a property-aware latent embedding space, RetroMPA consistently improves top-1 accuracy across eight representative retrosynthesis models by an average of 5.50% on USPTO-50K. Furthermore, we demonstrate its scalability by validating its performance on the large-scale USPTO-Full data set, achieving an average improvement of about 2.03% across both template-based and template-free architectures. In addition, wet-lab experiments provide preliminary support for the practical utility of the framework. These syntheses confirmed viable, previously unreported substrate combinations for established, classic reaction paradigms─specifically, the Suzuki–Miyaura coupling, the Bucherer reaction, and the Friedel–Crafts acylation, thereby suggesting that RetroMPA can operate beyond mere data fitting. The code is open-sourced at https://github.com/MengzhouLu/RetroMPA.