Proteomics‐Driven Strategies for Proximity‐Inducing Drug Discovery

Abstract

ABSTRACT In recent years, proximity‐inducing drugs have emerged as a novel therapeutic modality that induces or stabilizes protein‐protein interactions, especially by recruiting effector proteins to specific target proteins, thereby achieving functions beyond traditional inhibitors. The potential of proximity‐inducing drugs extends beyond targeted protein degradation (TPD), as studies have demonstrated their ability to regulate biological processes such as signal transduction, gene transcription, chromatin regulation, and protein trafficking by modulating protein interaction networks. Rational discovery of proximity‐inducing drugs requires clarifying their effects on protein‐protein interactions, determining drug selectivity, and developing suitable ligands for drug construction. Proteomics has become a central technology in drug discovery, enabling global identification of the direct drug targets and systematic characterization of proteome‐wide downstream responses. This provides a more refined map of drug mechanisms. In parallel, advances in machine learning applied to proteomic data, together with the expansion of proteome‐wide ligandability maps, are further accelerating the discovery and optimization of proximity‐inducing drugs. This review summarizes recent advances of proximity‐inducing drugs, with a particular emphasis on how proteomics facilitates target space expansion, drug efficacy optimization, and ligandability discovery, alongside the emerging contributions of machine learning. Collectively, these insights aim to support the rational development of next‐generation proximity‐inducing drugs.