A deep learning and digital archaeology approach for mosquito repellent discovery

Insect-borne diseases kill > 0.5 million people annually. Currently available repellents for personal or household protection are limited in their efficacy, applicability, and safety profile. Here, we describe a machine-learning-driven high-throughput method for the discovery of novel repellent molecules. To achieve this, we digitized a large, historic dataset containing ~19,000 mosquito repellency measurements. We then trained a graph neural network (GNN) to map molecular structure and repellency. We applied this model to select 317 candidate molecules to test in parallelizable behavioral assays, quantifying repellency in multiple insect vectors of the pathogens of disease and in follow-up trials with human volunteers. The GNN approach outperformed a chemoinformatic model and produced a hit rate that increased with training data size, suggesting that both model innovation and novel data collection were integral to predictive accuracy. We identified > 10 molecules with repellency similar to or greater than the most widely used repellents. We analyzed the neural responses from the mosquito antennal (olfactory) lobe to selected repellents and found strong responses to many of the tested compounds, including those predicted to be strong repellents. Results from the antennal lobe recordings also demonstrated a correlation between the evoked responses to strong repellents and our GNN representation. This approach enables computational screening of billions of possible molecules to identify empirically tractable numbers of candidate repellents, leading to accelerated progress towards solving a global health challenge.