Design and synthesis of bifunctional molecules for directing phosphorylation

Abstract

The field of bifunctional molecules such as PROTAC, DUBTAC and PhoRC has demonstrated that inducing proximity between two protein complexes is sufficient to redirect post-translational modifications (PTMs), and effect cellular functions. As phosphorylation plays a key role in many cellular functions such as cell growth, signalling and death, the ability to selectively and dose dependently direct phosphorylation of a target protein would be a novel and powerful chemical tool, complementary to kinase inhibitors. Our hypothesis is that rationally designed bifunctional molecules could redirect AMPK to phosphorylate neo-substrates by inducing proximity between a kinase and a target protein. The aim of this work is to show increased levels of phosphorylation of a target protein. Here we showed the development of bifunctional molecules, capable of binding AMP-activated protein kinase (AMPK) and target proteins. We used structural information to identify suitable solvent exposed sites on published AMPK small molecule activators, then designed and synthesised relevant compounds to test their activity. Likewise, a suitable ligand for target proteins was selected and a solvent exposed site identified and validated, and a library of bifunctional compounds synthesised using click chemistry. Testing these compounds in global unbiased phosphoproteomics has shown selective increase in phosphorylation at specific sites, which we sought to confirm with multiple techniques. We anticipate these functional compounds act through ternary complex formation and demonstrate selectivity based on the overall structure of the target protein. Furthermore, we hope that this work may provide a basis for this emerging method of directing phosphorylation.