A comprehensive review of emerging approaches in machine learning for de novo PROTAC design

Abstract

Targeted protein degradation (TPD) is a rapidly growing field in modern drug discovery that aims to regulate the intracellular levels of proteins by harnessing the cell's innate degradation pathways to selectively target and degrade disease-related proteins. This strategy creates new opportunities for therapeutic intervention in cases where occupancy-based inhibitors have not been successful. Proteolysis-targeting chimeras (PROTACs) are at the heart of TPD strategies, which leverage the ubiquitin–proteasome system for the selective targeting and proteasomal degradation of pathogenic proteins. This unique mechanism can be particularly useful for dealing with proteins that were once deemed “undruggable” using conventional small-molecule drugs. PROTACs are hetero-bifunctional molecules consisting of two ligands, connected by a chemical linker. As the field evolves, it becomes increasingly apparent that traditional methodologies for designing such complex molecules have limitations. This has led to the use of machine learning (ML) and generative modeling to improve and accelerate the development process. In this review, we aim to provide a thorough exploration of the impact of ML on de novo PROTAC design – an aspect of molecular design that has not been comprehensively reviewed despite its significance. Initially, we delve into the distinct characteristics of PROTAC linker design, underscoring the complexities required to create effective bifunctional molecules capable of TPD. We then examine how ML in the context of fragment-based drug design (FBDD), honed in the realm of small-molecule drug discovery, is paving the way for PROTAC linker design. Our review provides a critical evaluation of the limitations inherent in applying this method to the complex field of PROTAC development. Moreover, we review existing ML works applied to PROTAC design, highlighting pioneering efforts and, importantly, the limitations these studies face. By offering insights into the current state of PROTAC development and the integral role of ML in PROTAC design, we aim to provide valuable perspectives for biologists, chemists, and ML practitioners alike in their pursuit of better design strategies for this new modality.