Phosphoestamers: A new technology platform to block protein-protein interactions in the cell

Classical drug discovery involves designing a small molecule which will fit into a pocket on a target protein which has been identified due to its relationship to a disease. However, not all protein targets have pockets – many operate through protein-protein interactions (PPIs) which involve large, relatively flat protein surfaces. PPIs are involved in nearly every disease, and therefore affect everyone, but are of particular importance in cancer, infectious disease, and neurodegeneration. PPIs have been extremely difficult to drug with small molecules, because there is nowhere for them to fit. Proteins and peptides can act as inhibitors but are restricted in terms of their chemical structure and subject to recognition by biological process such as degradation. The ideal solution would be a large and structurally defined molecule, like a proteins itself, but with complete control over chemical structure which would allow fine-tuning of interactions and stability under biological conditions We have discovered that a family of synthetic chain molecules with a defined sequence of units (phosphoestamers) can be used to block PPIs using a newly developed process for selecting the right sequences out of hundreds of thousands of possibilities. We have demonstrated proof-of-principle in the identification of phosphoestamers which selectively block the interaction between a cancer-causing mutant form of the protein KRAS and its PPI partner RAF; a major longstanding therapeutic target in cancer. Our hit phosphoestamers were potent at low concentrations, and did not affect the non-mutant protein, providing a promising starting point for drug discovery. In principle, the selection process could be used to identify inhibitors of PPIs in any disease. However, phosphoestamers are not classically ‘drug-like’ molecules and will require strategies for delivery into cells, as is currently required for nucleic acid therapeutics, which they resemble in terms of chemistry. This project aims to develop phosphoestamers PPI inhibitors ready for use in preclinical drug discovery. To achieve this, we will broaden the range of phosphoestamer building blocks available, increase the size of the library to millions of sequences, and optimise the selection method. We will perform selections for PPI inhibitors taking three structurally and functionally diverse proteins, all involved in cancer, as exemplars. We will then measure and optimise phosphoestamer stability under biological conditions. Taking a range of cutting-edge technologies used currently to deliver nucleic acid therapeutics, we will establish the best way to deliver phosphoestamers into cells. We will then measure the efficacy and mechanism of phosphoestamers PPI inhibition inside cells. This will provide a strong grounding for targeted preclincal development. Establishment of phosphoestamers as a new therapeutic modality would have widespread and significant impacts. It would allow targeting of many previously inaccessible points in biochemical pathways which could result in a swathe of new treatments for previously intractable conditions. The model systems used herein relate to challenges in cancer and could lead to new drug candidates operating by unprecedented mechanisms. In the long term, there could be structural impact on pharmaceuticals: because activity relies on monomer sequence, many drugs could be made from a small set of monomers. This could open up new opportunities in point-of-care pharmaceutical production at remote sites, serving isolated, and disadvantaged communities around the world, or even future off-world communities, providing both human and economic benefit.