One Sequence, Many Decodings: CAGenMol-2 Recasts Drug Design as Masked Molecular Inference

Abstract

Drug design couples property evaluation, conditional generation, structure-based design, and local optimization, yet machine learning systems typically address these capabilities with separate task-specific models. We introduce CAGenMol-2, a masked diffusion molecular language model that represents molecules, continuous scalar properties, and 3D protein pockets within a single wrapped sequence. Within this pretrained interface, downstream operations are selected by which sequence regions are observed or masked at inference, allowing one checkpoint to perform property prediction, property- and pocket-conditioned generation, and partial-constraint design without task-specific architectures or backbone fine-tuning. We further propose Adaptive Fragment Optimization (AdaFO), a gradient-free mask-and-refill search that turns the masked decoder into an iterative local molecular optimizer. On CrossDocked2020, AdaFO increases Success Rate from 30.2\% to 70.8\%, the best reported under this protocol, while largely preserving drug-likeness and diversity. Finally, scaffold-preserving directional editing and CRBN/VHL case studies demonstrate its use in compound design workflows spanning local molecular editing, structure-based prioritization, and downstream simulation-based screening.