Development of robust and effective strategies for retrosynthetic planning requires a deep understanding of the synthesis process. A critical step in achieving this goal is accurately identifying synthetic intermediates. Current machine learning-based methods often overlook the valuable context from the overall route, focusing only on predicting reactants from the product, requiring cost annotations for every reaction step, and ignoring the multi-faced nature of molecular, resulting in inaccurate synthetic route predictions. Therefore, we introduce RetroInText, an advanced end-to-end framework based on a multimodal Large Language Model (LLM), featuring in-context learning with TEXT descriptions of synthetic routes. First, RetroInText including ChatGPT presents detailed descriptions of the reaction procedure. It learns the distinct compound representations in parallel with corresponding molecule encoders to extract multi-modal representations including 3D features. Subsequently, we propose an attention-based mechanism that offers a fusion module to complement these multi-modal representations with in-context learning and a fine-tuned language model for a single-step model. As a result, RetroInText accurately represents and effectively captures the complex relationship between molecules and the synthetic route. In experiments on the USPTO pathways dataset RetroBench, RetroInText outperforms state-of-the-art methods, achieving up to a 5% improvement in Top-1 test accuracy, particularly for long synthetic routes. These results demonstrate the superiority of RetroInText by integrating with context information over routes. They also demonstrate its potential for advancing pathway design and facilitating the development of organic chemistry. Code is available at https://github.com/guofei-tju/RetroInText.

MOTIVATION: Metabolic stability is crucial in the early stage of drug discovery and development. Drug candidate screening and optimization can be streamlined through the accurate prediction of stability. Functional groups within drug molecules are known as pharmacophores, which bind directly to receptors or biological macromolecules to produce biological effects, thereby affecting metabolic stability. Therefore, determining metabolic stability via the pharmacophore groups remains a significant challenge. RESULTS: To address these issues, we propose a Pharmacophore-guided Hypergraph representation framework for predicting metabolic Stability (HyperPhS). In this study, we introduce a hypergraph-based method to extract features from metabolic pharmacophores with multi-view representation and contrastive learning. In particular, we introduce a pharmacophore-based contrastive learning encoder that captures the consistency between functional and nonfunctional structures. Our method applies ChatGPT simultaneously to metabolites and heterogeneous encoders and integrates multimodal representations by using attention-driven fusion modules coupled with fully connected neural networks. On the HLM dataset, HyperPhS achieves outstanding performance with 87.6% in AUC and 62.6% in MCC, alongside an external test AUC of 88.3%. In addition, pharmacophore groups studied by HyperPhS are validated for their interpretability through case studies. Overall, HyperPhS is an effective and interpretable tool for determining metabolic stability, identifying critical functional groups, and optimizing compounds. AVAILABILITY AND IMPLEMENTATION: The code and data are available at https://github.com/xiaoyiliu-usc/HyperPhS.