The discovery of active compounds for novel, underexplored targets is essential for advancing innovative therapeutics across a wide range of diseases. Recent advancements in artificial intelligence (AI) are revolutionizing active compound discovery by dramatically enhancing the efficiency, accuracy, and scalability previously challenged by traditional methods. This review provides a comprehensive overview of AI-driven methodologies for active compound discovery, with a particular focus on their application to novel targets. Initially, we explore how AI overcomes traditional bottlenecks in molecular design, enabling precise protein perception through high-accuracy protein structure prediction and enhanced docking precision. Building upon these target-focused capabilities, AI-driven approaches also advance ligand exploration, effectively bridging biological and chemical spaces through sophisticated data transfer techniques that maximize the utility of available activity data. By assessing overall cellular or organismal responses, AI plays a pivotal role in decoding complex biological systems, driving phenotypic drug discovery (PDD) through multi-modal data integration. Finally, we discuss how AI is addressing challenges associated with targeting previously undruggable proteins, exemplified by the development of protein degraders. By synthesizing these cutting-edge advancements, this review serves as a valuable resource for researchers seeking to leverage AI in the discovery of next-generation therapeutics.