Designing a single molecule that modulates two targets is a promising strategy for polypharmacology, but it remains substantially harder than standard single-target generation because one candidate must satisfy two binding requirements while preserving drug-likeness and synthesizability. Existing dual-target generative methods typically introduce dual-target capability by either retraining the generator or intervening in the diffusion process during sampling. The former can be costly and difficult to stabilize when dual-target supervision is sparse, while the latter may be sensitive to denoising-time target balancing and competing update directions. These limitations motivate a generator-preserving alternative that keeps the pretrained prior intact: can dual-target candidates instead be recovered from the input space of a frozen single-target diffusion model, without modifying its parameters or denoising dynamics? We formulate this task as a constrained multi-objective optimization problem and propose REUSE, a hierarchical evolutionary input-space search framework that combines pair-conditioned exploration with structured multi-stage selection to enforce dual-target affinity, chemical quality, and diversity. Experiments show that, compared with methods that modify the diffusion process, REUSE consistently improves dual-target affinity and balance, achieving a 20.9-percentage-point gain in Dual High Affinity over the strongest prior baseline while maintaining competitive molecular quality.
Dual-target drug design aims to generate 3D molecules that can simultaneously interact with two target proteins, offering a promising route for discovering polypharmacological compounds against complex diseases. While recent generative models have shown encouraging performance in single-target drug design, existing dual-target approaches either focus on sequence generation or introduce an additional predictive drift term into the diffusion-based generative trajectory, which limits their ability to fully integrate feature information from both targets. We propose FusedBFN, a fused Bayesian flow network (BFN) for dual-target molecular design. FusedBFN formulates dual-target generation as distribution fusion in a unified continuous parameter space and employs a product-of-experts formulation to incorporate dual-target information throughout the generative process. To address the scarcity of dual-target structural data, we leverage a pretrained target-aware BFN model as the shared backbone. We further introduce a chemically aware prior-based alignment method and a prior-free pocket alignment strategy to construct aligned dual-target contexts. Extensive experiments demonstrate that FusedBFN generates molecules with strong binding affinity toward dual targets while maintaining favorable molecular properties.
Dual-target molecule generation, which focuses on discovering compounds capable of interacting with two target proteins, has garnered significant attention due to its potential for improving therapeutic efficiency, safety and resistance mitigation. Existing approaches face two critical challenges. First, by simplifying the complex dual-target optimization problem to scalarized combinations of individual objectives, they fail to capture important trade-offs between target engagement and molecular properties. Second, they typically do not integrate synthetic planning into the generative process. This highlights a need for more appropriate objective function design and synthesis-aware methodologies tailored to the dual-target molecule generation task. In this work, we propose CombiMOTS, a Pareto Monte Carlo Tree Search (PMCTS) framework that generates dual-target molecules. CombiMOTS is designed to explore a synthesizable fragment space while employing vectorized optimization constraints to encapsulate target affinity and physicochemical properties. Extensive experiments on real-world databases demonstrate that CombiMOTS produces novel dual-target molecules with high docking scores, enhanced diversity, and balanced pharmacological characteristics, showcasing its potential as a powerful tool for dual-target drug discovery. The code and data is accessible through https://github.com/Tibogoss/CombiMOTS.
Generating molecules that simultaneously satisfy drug-like properties and conform to the 3D structure of a target protein is a core challenge in structure-based drug design (SBDD). Existing generative approaches, however, often rely on costly post-hoc processing during Sampling or require carefully curated datasets during training, yet still achieve modest gains. These limitations are especially pronounced in multi-objective settings, where balancing conflicting criteria remains a core challenge. To address these challenges, We propose FTDiff, a reinforcement learning fine-tuning framework tailored for diffusion-based molecular generation under structural constraints. To ensure stable and sample-efficient optimization, FTDiff adopts a group relative policy optimization (GRPO) style strategy. Furthermore, FTDiff builds upon a time-free pretrained diffusion model and incorporates a fast sampling mechanism that reduces the number of denoising steps, significantly accelerating both training and inference while maintaining generation quality. By optimizing a fixed threshold-aware reward, FTDiff effectively guides the model to produce valid, diverse, and high- quality molecules that balance multiple drug design objectives. Extensive experiments on benchmark datasets demonstrate that FTDiff consistently outperforms prior methods, without requiring expensive post-hoc optimization or intricate data engineering.