From part to whole: AI-driven progress in fragment-based drug discovery

Fragment-based drug discovery is a technique that finds potent binding fragments to the binding hotspots and makes them a hit compound. The combination of fragments allows us to explore the large chemical space. Thus, it becomes an effective methodology for identifying lead compounds. Three concepts have been introduced to make the fragments into the compound: growing, merging, and linking. Recently, growing and merging techniques using AI have significantly improved the accuracy and efficiency of molecular design. In this review, recent techniques such as VAE, reinforcement learning, and SE(3)-equivariant models will be discussed. These methods enable precise molecular structure exploration and optimization. Additionally, we address techniques utilizing diffusion models, language models, and deep evolutionary learning. We also introduce linker optimization methods using reinforcement learning and deep learning-based models. This progress of fragment-based drug discovery methods with AI opens the possibility of discovering the vast chemical space with high efficiency.