PROTACS: new computational methods and targets

PROtealysis TArgeting Chimeras, also designated PROTACs, are bifunctional molecules composed of two protein ligands connected by a linker. The ligand on one side binds to the E3-ubiquitin ligase, which targets a protein for degradation, while the other ligand binds the unwanted proteins that needs to be removed from the cell. Since PROTACs had first been described in 2001, the technology has been applied to an increasing range of targets, with the first cancer therapeutics now in clinical trials.
All PROTACs are based on known ligands for an E3-ligase on one side, in many cases, the Von Hippel-Lindau tumor suppressor (VHL) connected to a known or novel ligand for the target protein. However, only recently, it has become clear that the length and chemistry of the linker, in most cases composed of polyethylene glycols, or alkyls, alkynes or triazoles, plays a major role in the biological activity of the PROTAC compound. With a virtually unlimited number of potential linkers, new computational methods are needed to guide and support the development of new PROTACs.
In this collaboration with the Cambridge Crystallographic Data Centre (CCDC) we will develop molecular modelling tools for linker design that use the structures of the VHL ligase and the target protein in combination with empirical rules derived from successful linkers. These tools will initially be tested and validated using one well-established PROTACs model system, VHL bound to the human bromodomain 4 (Brd4), a major target for cancer therapies, where crystals structures of the ternary VHL-PROTAC-Brd4 complex have been determined. In parallel we will target the Eppstein-Barr virus nuclear antigen 1 (EBNA1), the key protein, consistently expressed in all human tumours that are linked to Eppstein-Barr viral infections.
Several VHL and Brd4 ligands have been described in the literature and are commercially available. New PROTAC compound containing novel linkers will be synthesized in collaboration with the organic chemistry groups in the department. Binding to both, the VHL as well as the target protein, will be tested using the novel spectral-shift technology implemented in Nanotemper Dianthus screening. The high sensitivity of this techniques makes it particularly useful to investigate consecutive binding events in ternary systems in 384-well plate high-throughput format. The most promising compounds will be forwarded to our structural biology platform including crystallisation and crystal structure determination as well as cryo Electron Microscopy.