RIDE: Reference-Anchored Inference-Time Diffusion Editing for Scaffold Hopping

arXiv:2609.35623v1 Announce Type: cross Abstract: Scaffold hopping is a critical task in drug discovery, which seeks to discover new, structurally distinct molecules that share key functional groups and similar 3D shape with a reference binding ligand. Existing diffusion-based scaffold hopping methods formulate the problem as conditional generation of scaffolds given the functional groups. However, they lack a principled mechanism to jointly enforce 2D structural novelty and preserve the 3D shape of the reference ligand. Here, we introduce RIDE, a Reference-anchored Inference-time Diffusion Editing framework for scaffold hopping. RIDE recovers the reference diffusion noise trajectory conditioned on the binding pocket and functional groups, selects an optimal trajectory segment for editing via noise perturbation, and conducts a value-guided scaffold sampling to generate new scaffolds. Extensive experimental results demonstrate that, compared to baselines, RIDE consistently generates scaffolds with lower 2D similarity and higher 3D similarity to the reference, with an average improvements of 11.7% and 7.3%, respectively. Further analysis reveals that RIDE can accommodate various reward functions, and can preserve 3D similarity even when this is not explicitly included in the reward. Two case studies illustrate RIDE's ability to generate distinct scaffolds with different structures and properties, and its ability to introduce substantial 2D variation while maintaining very high 3D similarity. RIDE is publicly available at https://anonymous.4open.science/r/RIDE-C8A0.

Abstract:Scaffold hopping is a critical task in drug discovery, which seeks to discover new, structurally distinct molecules that share key functional groups and similar 3D shape with a reference binding ligand. Existing diffusion-based scaffold hopping methods formulate the problem as conditional generation of scaffolds given the functional groups. However, they lack a principled mechanism to jointly enforce 2D structural novelty and preserve the 3D shape of the reference ligand. Here, we introduce RIDE, a Reference-anchored Inference-time Diffusion Editing framework for scaffold hopping. RIDE recovers the reference diffusion noise trajectory conditioned on the binding pocket and functional groups, selects an optimal trajectory segment for editing via noise perturbation, and conducts a value-guided scaffold sampling to generate new scaffolds. Extensive experimental results demonstrate that, compared to baselines, RIDE consistently generates scaffolds with lower 2D similarity and higher 3D similarity to the reference, with an average improvements of 11.7% and 7.3%, respectively. Further analysis reveals that RIDE can accommodate various reward functions, and can preserve 3D similarity even when this is not explicitly included in the reward. Two case studies illustrate RIDE's ability to generate distinct scaffolds with different structures and properties, and its ability to introduce substantial 2D variation while maintaining very high 3D similarity. RIDE is publicly available at this https URL.

Artificial Intelligence (cs.AI); Machine Learning (cs.LG)

arXiv:2609.35623 [cs.AI]

(or arXiv:2609.35623v1 [cs.AI] for this version)

https://doi.org/10.48550/arXiv.2609.35623 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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RIDE: Reference-Anchored Inference-Time Diffusion Editing for Scaffold Hopping

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