High throughput bio-layer interferometry at Dundee for anti-microbial and interaction studies.

Proteins are at the centre of almost all the molecular processes that are important for the survival of the living cell, be that cell a free living microbe or part of a vital organ in a complex animal. The number and amount of different proteins in a cell is staggering but in order to successfully carry out their biological function, proteins must interact with exquisitely specific protein or chemical partners. Sometimes, forming a higher-order complex with other proteins is the central event to the biological process in question. Sometimes, proteins do not interact with other proteins at all but instead bind with small molecules, or other macromolecules such as nucleic acids, lipids or carbohydrates, before they can carry out their biological function. Understanding how proteins interact with other molecules is central to our basic understanding communication and signalling at the molecular level. Physicists, working in collaboration with biologists, chemists and mathematicians, have devised many techniques for measuring and quantifying molecular interactions. One relatively new technique is called bio-layer interferometry. In this technique a tiny fibre optic thread has a protein-of-interest attached to its tip. When this tip is dipped in a solution that contains a molecule that will interact with the protein-of-interest the optical properties of the fibre change and this can be recorded by the instrument. The data generated can therefore give brand new fundamental information on how proteins operate.

On the other hand, this instrumentation can also be of use in exploring for different chemicals that might disrupt protein-protein interactions or stop a protein from working altogether. The optical fibres are so small that they can be arranged in arrays of up to 96 fibres at a time. The fibres can then be dipped in hundreds of different chemicals over the course of a few minutes and that way huge 'chemical libraries' can be searched for random molecules that bind. From that narrowed-down set of interactors, it may be possible to find some that inhibit the activity of the protein-of-interest. So-called chemical 'inhibitors' that disrupt key cellular pathways are of critical importance in modern cell biology research projects, where they are used to understand fundamental aspects of cellular physiology. At Dundee, we also wish to use this instrument to search for molecules that might inhibit key process in microbial metabolism - and so help underpin the global search for new anti-microbials.

High throughput bio-layer interferometry has a growing reputation as a sophisticated and powerful tool that is perfectly suited to fundamental studies of protein-protein, protein-nucleic acid, and other protein-ligand interactions. Indeed, bio-layer interferometry seems set to become a major component in the modern drug discovery process providing key early-stage information during hit discovery programs and pre-clinical drug development. Research programs in the College of Life Sciences at Dundee are deeply involved in all of these areas. The recent investment by Dundee in structural biology, molecular microbiology, computational biology and drug discovery, including the building of the new £12.5M Centre for Translational and Interdisciplinary Research, has seen interest in this technique increasing exponentially.

The research outlined in this proposal focuses on two timely areas:

1. Combatting anti-microbial resistance: underpinning the development of anti-microbials

2. World class bioscience: advances in understanding protein-protein and protein-ligand interactions

The research strengths in microbiology at Dundee (covering bacteria, fungi, protozoan parasites and oomycete plant pathogens), when taken together with the unique expertise available in early-stage drug discovery and structure-based drug design, provide a powerful environment for tackling the growing threat of anti-microbial resistance.

In addition, Dundee is a recognised centre for high quality basic life sciences research. Fundamental studies of protein-protein, protein-nucleic acid, and other protein-ligand interactions, are central to much of the work currently undertaken. New capacity in high throughput bio-layer interferometry would enhance this research effort still further as well as seeding new academic and industrial collaborations.

Who will benefit and why?

1) Biotech companies interested in antimicrobial resistance, bacterial virulence, anti-infectives, biofilm formation, protein-protein recognition, and post-translational modifications. Such companies will benefit from the research programmes using this new instrument since it will generate new knowledge on interacting compounds, inhibitors and basic protein biochemistry. Projects will also report on the virulence of a key plant, animal and human pathogens. We will act to protect any intellectual property and to maximise opportunities for collaborative research or licensing. The Dundee research and innovation team have a wealth of industrial contacts and close links to Scottish Enterprise, and will help maximise the impact of all findings of commercial value. As and when appropriate, results will be peer-reviewed and published. Researchers interested in the instrumentation at Dundee already have strong contacts with industry, including GlaxoSmithKline (e.g. Protein Degradation DPU), LIONEX, Ubiquigent, Micromatrices, Cellexus).

2) Members of the wider academic community. Fellow academics and industrial partners are welcome to use our new instrumentation, and we can point to a long track record of successful collaborations. The primary mechanism for communication of research associated with collaborations will be through publication in peer review international journals. Open access publishing options will be used where BBSRC research is involved. The University of Dundee Library & Learning Centre holds funds for making RCUK research open access. In addition, we will liaise at the time of publication with the University of Dundee and BBSRC Press offices to ensure publicity of results of interest to the general public.

3) The staff employed on this project. The University of Dundee takes training of early career researchers seriously, thereby ensuring a successful contribution to the knowledge-led economy of UK Plc. There will be opportunities for undergraduate, postgraduate, postdoctoral training on this instrument - as well as visiting scientists. Resultant data will be presented at major research conferences, facilitating their career development through the acquisition and refining of key presentational and networking skills. In addition, the University of Dundee has an annual appraisal scheme to actively facilitate the career development of staff, including PDs and PIs. The PDs will also be encouraged to design and supervise undergraduate projects using this new technology, as well as to become involved in science communication.

4) The general public. It is important that members of the general public are aware and supportive of how tax payers' money is spent on scientific research. Therefore, as part of publicising the research projects using this new instrument, we will engage with local communities, through face-to-face discussion of our work and family-focused scientific event days. All the PIs backing this proposal are experienced science communicators, and the Dundee Open Doors Day in November will allow the public to see the new instrumentation in action first-hand.