Prediction of interactions between the SARS-CoV-2 ORF3a protein and small-molecule ligands using the ANDSystem cognitive platform, graph neural networks, and molecular modeling.

In recent years, artificial intelligence methods based on the analysis of heterogeneous graphs of biomedical networks have become widely used for predicting molecular interactions. In particular, graph neural networks (GNNs) effectively identify missing edges in gene networks - such as protein-protein interaction, gene-disease, drug-target, and other networks - thereby enabling the prediction of new biological relationships. To reconstruct gene networks, cognitive systems for automatic text mining of scientific publications and databases are often employed. One such AI-driven platform, ANDSystem, is designed for automatic knowledge extraction of molecular interactions and, on this basis, the reconstruction of associative gene networks. The ANDSystem knowledge base contains information on more than 100 million interactions among diverse molecular genetic entities (genes, proteins, metabolites, drugs, etc.). The interactions span a wide range of types: regulatory relationships, physical interactions (protein-protein, protein-ligand), catalytic and chemical reactions, and associations among genes, phenotypes, diseases, and more. In the present study, we applied attention-based graph neural networks trained on the ANDSystem knowledge graph to predict new edges between proteins and ligands and to identify potential ligands for the SARS-CoV-2 ORF3a protein. The accessory protein ORF3a plays an important role in viral pathogenesis through ion-channel activity, induction of apoptosis, and the ability to modulate endolysosomal processes and the host innate immune response. Despite this broad functional spectrum, ORF3a has been explored far less as a pharmacological target than other viral proteins. Using a graph neural network, we predicted five small molecules of different origins (metabolites and a drug) that potentially interact with ORF3a: N-acetyl-D-glucosamine, 4-(benzoylamino)benzoic acid, austocystin D, bictegravirum, and L-threonine. Molecular docking and MM/GBSA affinity estimation indicate the potential ability of these compounds to form complexes with ORF3a. Localization analysis showed that the binding sites of bictegravir and 4-(benzoylamino)benzoic acid lie in a cytosolic surface pocket of the protein that is solvent-exposed; L-threonine binds within the intersubunit cleft of the dimer; and austocystin D and N-acetyl-D-glucosamine are positioned at the boundary between the cytosolic surface and the transmembrane region. The accessibility of these binding sites may be reduced by the influence of the lipid bilayer. The binding energetics for bictegravirum were more favorable than for 4-(benzoylamino)benzoic acid (docking score -7.37 kcal/mol; MM/GBSA ΔG -14.71 ± 3.12 kcal/mol), making bictegravirum a promising candidate for repurposing as an ORF3a inhibitor.