In silico modeling of targeted protein degradation

Targeted protein degradation (TPD) techniques, particularly proteolysis-targeting chimeras (PROTAC) and molecular glue degraders (MGD), have offered novel strategies in drug discovery. With rapid advancement of computer-aided drug design (CADD) and artificial intelligence-driven drug discovery (AIDD) in the biomedical field, a major focus has become how to effectively integrate these technologies into the TPD drug discovery pipeline to accelerate development, shorten timelines, and reduce costs. Currently, the main research directions for applying CADD and AIDD in TPD include: 1) ternary complex modeling; 2) linker generation; 3) strategies to predict degrader targets, activities and ADME/T properties; 4) In silico degrader design and discovery. Models developed in these areas play a crucial role in target identification, drug design, and optimization at various stages of the discovery process. However, the limited size and quality of datasets related to TPD present challenges, leaving room for further improvement in these models. TPD involves the complex ubiquitin-proteasome system, with numerous factors influencing outcomes. Most current models adopt a static perspective to interpret and predict relevant tasks. In the future, it may be necessary to shift toward dynamic approaches that better capture the intricate relationships among these components. Furthermore, incorporating new and diverse chemical spaces will enhance the precision design and application of TPD agents.