Beyond the genome: proteome engineering for biological and drug discovery

A York graduate, Paul has worked on cell cycle control by protein phosphorylation (PhD with Phil Cohen and Carl Smythe, Dundee) and on the regulated transport of proteins across the nuclear envelope in yeast cells (post-doc with Pamela Silver, Harvard Med School/Dana Farber Cancer Institute funded by a Fellowship from the Human Frontiers Science Progamme). He established the Peptide Aptamer Group at the MRC Cancer Cell Unit in Cambridge as a tenure track Programme Leader, developing a next-generation scaffold for the presentation of constrained peptides that is now widely used in academia and in industry. In 2007 he moved to the University of Leeds as a Senior Lecturer where he went on to found and co-found two University spin-out companies, one of which (Avacta Life Sciences) now employs more than 80 people in the UK and the US. In 2017 he established his first start-up, metaLinear Ltd, whose mission is to use the scaffold technology inside cells (“proteome engineering”), to uncover vulnerable protein isoforms as new drug targets, and to guide the development of small molecule protein interaction inhibitors to combat antibiotic resistance.    

 

At the molecular level, biology is largely driven by protein interactions and the complexity of life is explained by proteomes, not by genomes. The detection of a transcript does not predict the presence of a protein, let alone how its shape, activity or partnerships may be affected by post-translational modifications (PTMs). Descriptive lists of proteins expressed in different cell types and protein-protein interaction maps both come with caveats around population heterogeneity, sub-cellular localisation and temporal fluxes.

To address some of these limitations, we have developed a platform that allows for the high throughput disruption of proteins in living cells. The core principle is that the best tool for the isolation and study of a protein will be another protein, as illustrated by the exquisite specificity and high binding affinities of antibodies. Because antibodies are not suited to the intracellular environments of most organisms, many groups have developed non-antibody binding proteins, sometimes called peptide aptamers. These consist of a protein or self-folding protein domain, called the scaffold, that can be used to present a variety of engineered amino acid sequences as surfaces for molecular interactions. We have taken this one step further, by ensuring that the scaffold itself has no detectable biological activity in the system under study. Our tools were conceived with the goal of bridging the gaps between the reductionist approaches of genetics, biochemistry and cell biology. We are now able to use a single reagent to (1) create a new phenotype, by changing the behaviour of a protein inside a cell rather than by targeting a gene; (2) affinity-purify the targeted protein for biochemical analysis including mass spectrometry and co-crystallography and (3) localise the protein in the cell of origin using fluorescence microscopy.

In this talk I will briefly cover the early protein engineering work and illustrate some of the key applications from the literature. I will describe how we have been able to use a phenotypic screen to discover, identify and validate novel drug targets in pathogenic E. coli and antibiotic-resistant bacteria, and will end with a discussion of how this technology may be applied in other organisms, including those used with the Department.