In recent years, artificial intelligence has been widely applied in the field of drug discovery, becoming deeply integrated into all stages of drug research and development and bringing new opportunities to the advancement of biomedicine. However, the application of artificial intelligence also comes with numerous challenges that require in-depth study and response. We focus on the three main stages of drug development: target discovery, de novo drug design, and the discovery and optimization of lead compounds. By incorporating cutting-edge application examples, we explore the challenges and future directions of artificial intelligence in drug research and development.