PIFT：用扩散与流匹配联合引导将肽-靶点相互作用模式迁移至小分子

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Abstract:Generating small molecules to target protein-protein interactions (PPIs) remains one of the most challenging yet high-reward frontiers in drug discovery. Unlike traditional small-molecule drugs that bind to deep, well-defined pockets, PPI interfaces often comprise broad, shallow binding surfaces. A natural strategy is to leverage known peptide-target interactions, as peptide ligands provide rich interface-level constraints. However, a major algorithmic challenge is that rigid atom-level conditioning on peptide structures can over-constrain the generative space and exclude valid small-molecule solutions. To address this challenge, we present PIFT (Peptide InterFace Transfer), a novel framework that transfers peptide-target interaction patterns to small molecules through joint sampling-time guidance of masked discrete diffusion and continuous flow matching. PIFT first maps peptide-target and small-molecule-target interfaces into a shared, target-conditioned interaction space, capturing transferable interface information across molecular modalities. The resulting peptide-derived reference then jointly steers building-block logits and 3D coordinates toward peptide-compatible molecules while preserving a strong adapted molecular prior. Extensive experiments across diverse PPI targets show that the learned representation captures cross-modal interaction compatibility, while peptide guidance improves interface recovery and achieves strong docking performance and favorable molecular properties.

Submission history

From: Jian Lee [view email]
[v1] Fri, 30 Oct 2026 06:33:09 UTC (4,840 KB)