De novo generation of dual-target compounds using artificial intelligence
K. Yasuda, Francois Berenger, Kazuma Amaike, Ayaka Ueda, Tomoya Nakagomi, Genki Hamasaki, Chen Li, Noriko Otani, Kazuma Kaitoh, Koji Tsuda, Kenichiro Itami, Yoshihiro Yamanishi
Abstract
Drugs that interact with multiple therapeutic targets are potential high-value products in polypharmacology-based drug discovery, but the rational design remains a formidable challenge. Here, we present artificial intelligence (AI)-based methods to design the chemical structures of compounds that interact with multiple therapeutic target proteins. The molecular structure generation is performed by a fragment-based approach using a genetic algorithm with chemical substructures and a deep learning approach using reinforcement learning with stochastic policy gradients in the framework of generative adversarial networks. Using the proposed methods, we designed the chemical structures of compounds that would interact with two therapeutic targets of bronchial asthma, i.e., adenosine A2a receptor (ADORA2A) and phosphodiesterase 4D (PDE4D). We then synthesized 10 compounds and evaluated their bioactivities via the binding assays of 39 target human proteins, including ADORA2A and PDE4D. Three of the 10 synthesized compounds successfully interacted with ADORA2A and PDE4D with high specificity.