De novo drug design based on patient gene expression profiles via deep learning

Computational de novo drug design is a challenging issue in medicine, and it is desirable to consider all of the relevant information of the biological systems in a disease state. Here, we propose a novel computational method to generate drug candidate molecular structures from patient gene expression profiles via deep learning, which we call DRAGONET. Our model can generate new molecules that are likely to counteract disease-specific gene expression patterns in patients, which is made possible by exploring the latent space constructed by a transformer-based variational autoencoder and integrating the substructures of disease-correlated molecules. We applied DRAGONET to generate drug candidate molecules for gastric cancer, atopic dermatitis, and Alzheimer's disease, and demonstrated that the newly generated molecules were chemically similar to registered drugs for each disease. This approach is applicable to diseases with unknown therapeutic target proteins and will make a significant contribution to the field of precision medicine.