DNA-encoded library (DEL) technology has emerged as a transformative platform in early-stage drug discovery, enabling the rapid and cost-effective exploration of ultra-large chemical spaces. However, identifying ligands for challenging targets characterized by featureless surfaces, high conformational plasticity, or shallow binding sites remains a formidable challenge. While the potential of DEL is widely recognized, a systematic evaluation of its strategic evolution against these intractable targets over the past fifteen years is timely. This review surveys the progress of DEL technology in tackling such targets, organized by GTPases, epigenetic regulators, phosphatases, protein–protein interaction (PPI), membrane proteins, and RNA. We highlight pivotal case studies and methodological breakthroughs while critically examining aspects of driving force in DEL such as DNA-compatible chemistry, diversified library design, advanced selection strategies, and artificial intelligence (AI) integration. Finally, we illustrate how DEL evolves from a conventional screening tool into a multifaceted discovery engine. By identifying future directions that include expanding three-dimensional chemical space, enhancing library fidelity, and deepening integration with functional biology and AI, this review provides a strategic roadmap to inspire and guide future DEL campaigns against those challenging targets. • Challenging targets are biological targets that are difficult to modulate using conventional drug discovery approaches. • This review systematically presents case studies demonstrating DELs’ successful identification of ligands against challenging targets. • Advances in chemical space expansion, library design, selection methods, and integration of artificial intelligence are expected to empower DEL technology to target currently unexplored challenging targets.
Du et al. (Sun,) studied this question.