TACFormer: Transformer-Based Generative Model for Target-Conditioned De Novo PROTAC Design

Abstract

Targeted protein degradation (TPD) represents a fundamental shift in drug discovery, moving beyond traditional target inhibition toward the event-driven removal of disease-causing proteins. A prominent strategy for TPD is the use of proteolysis-targeting chimeras (PROTACs), heterobifunctional molecules that selectively route a protein of interest (POI) to the ubiquitin-proteasome system for degradation. While PROTAC design still relies heavily on trial-and-error synthesis and experimental testing, deep generative models offer a promising means to explore PROTAC chemical space in silico and generate novel molecules. However, many existing generative methods formulate PROTAC design primarily as a linker-generation problem, with POI-binding (warhead) and E3-ligase-binding components fixed in advance. This restricts exploration of the full PROTAC chemical space and often leaves the POI implicit through the predefined warhead, rather than using protein-level information as an explicit conditioning signal during generation. To address these limitations, we propose TACFormer: a transformer-based generative model for target-aware de novo PROTAC design. The model conditions a GPT-style molecular decoder on pretrained ESM-2 representations of POI sequences, allowing POI-level information to steer full-molecule generation. Our results show that TACFormer generates highly novel and chemically diverse PROTACs while showing consistent POI-dependent shifts in generated chemical space. In particular, molecules generated under specific target conditions preferentially populate chemical neighborhoods associated with POIs in the held-out dataset, while extrapolating to novel chemotypes. By natively integrating biological context into the generative process, TACFormer moves PROTAC design toward a more biology-informed exploration of degrader chemical space.