Structure-Based PROTAC Design In-Silico

Proteolysis Targeting Chimeras (PROTACs) are small molecules that induce the degradation of target proteins of interest and have shown considerable promise as novel therapeutic agents.

PROTACs are heterobifunctional compounds containing one moiety that binds to the target protein of interest and one that binds to an E3 ubiquitin ligase. Recruitment of the E3 ligase leads to ubiquitination and subsequent degradation of the target by the proteasome.

The design of PROTACs largely remains an empirical process because of an insufficient understanding of the molecular basis for productive recruitment of target and E3 ligase into a ternary complex.

Furthermore, there are only a handful of small-molecule ligands for E3 ligases that are amenable for PROTAC conjugation, so expanding the chemical space to PROTAC design is an important direction for the field.

Virtual screening and structure-based drug design are powerful approaches for designing of drug-like molecules but their application to PROTAC design is still in its infancy.

The structural complexity of the ternary complex central to PROTAC activity, and the chemical complexity of PROTAC molecules, are amongst some of the main challenges to structure-based PROTAC design.

The goal of this proposal is to develop novel methodologies to contribute to systematically address these important challenges.

The long-term goal of this proposal is to develop structure-based PROTAC design as an efficient, universally applicable platform for prediction, designing, and screening of effective PROTAC degraders of target proteins.

The success in this project will pave the way to efficiently degrading “undruggable” targets as a powerful new modality of chemical intervention into biology and disease.