Abstract
Environmental sustainability is increasingly recognized as a critical consideration in pharmaceutical development, yet it is rarely incorporated at the scale of molecular-level design. This study introduces a strategy to predict cradle-to-gate indicators that can be flexibly incorporated into multiple early-stage molecular prioritization scenarios. A dataset of 150 pharmaceutical-relevant molecules was compiled, with each molecule described by structural descriptors, thermophysical properties, and ReCiPe endpoint indicators representing human health, ecosystem quality, and resource scarcity. A dual-branch multi-task model combining graph-based and descriptor-based representations was trained to predict these three endpoint indicators. Model performance was evaluated through validation metrics, local sensitivity analysis, and SHAP-based interpretability. A case study with solubility-based feasibility constraints was then used to illustrate how different sustainability weighting schemes affect molecular ranking and to demonstrate the potential for incorporating sustainability assessment into early-stage molecular prioritization. The results indicate that sustainability preferences can lead to distinct prioritization patterns, while some candidates remain comparatively favourable across scenarios.