Structure-guided compound prioritization strategy for virtual screening identifies putative binders for the nuclear receptor LRH-1

Abstract

Compound ranking in structure-based virtual screening notoriously yields highly ranked false positive binders due to variable poses or biases in scoring terms. We developed a compound prioritization strategy that utilizes sampled docked poses from contrasting docking approaches (targeted physics-based docking and blind docking with a generative model) against multiple models of the target protein to train a multi-layer perceptron (MLP). The model predicts binders at the orthosteric ligand-binding pocket of the nuclear receptor LRH-1 (NR5A2). Our approach circumvents the reliance on a single docked pose for scoring compounds or individual scoring metrics for compound ranking. In a separate benchmarking set, we observed that the MLP identifies known binders that are chemically dissimilar from the compounds in the training set and is sensitive to single scaffold modifications, making it a potential tool for lead optimization. We applied our strategy to a prospective virtual screening campaign, which resulted in the discovery of four putative LRH-1 binders. We found that a combination of scoring and prediction metrics enriches for the hit compounds across library sizes. In all, this implementation presents a method to leverage structural and experimental data to aid virtual screening for a challenging protein target.