Unleashing the power of DNA-encoded libraries for challenging targets in drug discovery

TL;DR

This review explores how DNA-encoded libraries (DELs) are being used to discover drugs for difficult biological targets that are hard to tackle with traditional methods.

Contribution

The paper provides a systematic review of DEL advancements and strategies for challenging targets over the past 15 years.

Findings

DELs have successfully identified ligands for challenging targets like GTPases and membrane proteins.

Advances in DNA-compatible chemistry and AI integration are enhancing DEL effectiveness.

DEL technology is evolving into a multifaceted discovery engine beyond conventional screening.

Abstract

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.

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•Challenging targets are biological targets that are difficult to modulate using conventional drug discovery approaches.•This review presents case studies demonstrating DELs’ successful identification of ligands against challenging targets.•Advances in chemical space, library design, selection methods, and AI will empower DEL to target challenging targets.

Challenging targets are biological targets that are difficult to modulate using conventional drug discovery approaches.

This review presents case studies demonstrating DELs’ successful identification of ligands against challenging targets.

Advances in chemical space, library design, selection methods, and AI will empower DEL to target challenging targets.

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