End-to-End Reverse Screening Identifies Protein Targets of Small Molecules Using HelixFold3

TL;DR

This paper introduces an end-to-end reverse screening method using HelixFold3, a high-accuracy structure prediction model, to improve protein target identification for small molecules in drug discovery.

Contribution

The study presents a novel integrated framework that models protein folding and ligand docking simultaneously, enhancing accuracy over traditional step-wise reverse screening approaches.

Findings

Improved screening accuracy compared to conventional methods.

Enhanced structural fidelity and binding-site precision.

Effective in target prioritization for diverse small molecules.

Abstract

Identifying protein targets for small molecules, or reverse screening, is essential for understanding drug action, guiding compound repurposing, predicting off-target effects, and elucidating the molecular mechanisms of bioactive compounds. Despite its critical role, reverse screening remains challenging because accurately capturing interactions between a small molecule and structurally diverse proteins is inherently complex, and conventional step-wise workflows often propagate errors across decoupled steps such as target structure modeling, pocket identification, docking, and scoring. Here, we present an end-to-end reverse screening strategy leveraging HelixFold3, a high-accuracy biomolecular structure prediction model akin to AlphaFold3, which simultaneously models the folding of proteins from a protein library and the docking of small-molecule ligands within a unified framework. We validate this approach on a diverse and representative set of approximately one hundred small molecules. Compared with conventional reverse docking, our method improves screening accuracy and demonstrates enhanced structural fidelity, binding-site precision, and target prioritization. By systematically linking small molecules to their protein targets, this framework establishes a scalable and straightforward platform for dissecting molecular mechanisms, exploring off-target interactions, and supporting rational drug discovery.