DeorphaNN: Virtual screening of GPCR peptide agonists using AlphaFold-predicted active state complexes and deep learning embeddings

Abstract

Peptide-activated G protein-coupled receptors (GPCRs) regulate critical physiological processes such as metabolism, neural signalling, and endocrine function through their interaction with neuropeptides and peptide hormones. Despite their importance, identifying endogenous peptide agonists for GPCRs remains challenging, particularly for orphan receptors without known ligands. Recent advances in deep learning-based protein structure prediction, exemplified by AlphaFold (AF), have shown application beyond structural modelling, including protein-protein interaction prediction. Given that GPCR-peptide agonist interactions represent a specialized form of protein-protein interaction, we leveraged a dataset of experimentally validated agonist and non-agonist GPCR-peptide interactions from Caenorhabditis elegans to evaluate AF-Multimers ability to distinguish agonist-bound complexes. When modelling GPCR-peptide complexes, AF-Multimer confidence metrics partially discriminate agonist from non-agonist interactions, with improved discrimination achieved by utilizing AF-Multistate-derived active-state templates. We further investigated whether embeddings from the hidden layer of AF-Multimers neural network could distinguish agonist from non-agonist complexes. Feature performance analysis reveals that AF- Multimers pair representations outperform single representations, with distinct subregions of the pair representation providing complementary predictive signals. Building on these insights, we developed DeorphaNN, a graph neural network integrating active-state GPCR-peptide structural predictions, interatomic interactions, and deep learning embeddings to prioritize GPCR-peptide agonist interactions. DeorphaNN generalizes across datasets derived from different species, including annelids and humans, and successfully uncovered peptide agonists for two orphan GPCRs. DeorphaNN offers a novel computational resource to accelerate deorphanization by prioritizing GPCR-peptide agonist candidates for AI-guided experimental validation.