Protein aptamers to enable structure-based drug discovery - making the undruggable druggable

Protein aptamers (PAs eg. Affimers, nanobodies and DARPins) are molecules which can recognise and bind to proteins to help visualise and study them. They can be modified to bind specific targets and have been shown to be as effective as antibodies for this application. However PAs also offer many advantages over antibodies, including better stability, improved ability to reach a range of tissues within the body, and simpler production.
There are many potential applications for PAs within the fields of drug discovery and structural biology. They could be used to capture targets onto a solid surface or associated with a fluorescent chemical probe to carry out drug binding experiments. PAs could also be attached to a target to alter its properties and make it more amenable structural determination by current methods.

The primary aim of this project is to use PAs known as DARPins to aid the drug discovery process by facilitating the visualisation of small targets usually unsuitable for imaging by cryo EM. Cryo EM is a method by which biological specimens are observed using an electron microscope. Many intracellular proteins cannot currently be visualised by cryo EM due to their small size. DARPins consist of repeating modules, the number of which can be altered depending on the application to produce either small or large DARPins. They also have a rigid, helical structure when several repeating units are bound together. Therefore attaching DARPins through protein engineering to smaller protein targets could make them amenable to imaging via cryo EM by adding bulk and stability. This would offer a technological solution to biological problem through exploiting understanding of structural biology and protein-protein interactions.

Following evaluation of DARPin scaffolds for imaging of known targets using cryo EM, the same method will be evaluated for imaging of novel drug targets with structures that remain unsolved. This will include targets which would be considered difficult to prosecute by other means, again due to their small size, flexibility or incompatibility with other structural methods. A cyclic peptides library will be screened against targets of interest, with the resultant high affinity cyclic peptides engineered on to the DARPin scaffold. The DARPin scaffold-target complex will then be used to determine the structure of the target using cryo EM.

The overall aim is to implement this methodology of using PAs to enable cryo EM within the Newcastle University Center for Cancer drug discovery programme, in order to improve the interrogation of potential drug targets and facilitate structure based drug discovery.

The CDT has five primary beneficiaries:
The CDT cohort
Our students will receive an innovative training experience making them highly employable and equipping them with the necessary knowledge and skillset in science and enterprise to become future innovators and leaders. The potential for careers in the field is substantial and students graduating from the CDT will be sought after by employers. The Life Sciences Industrial strategy states that nearly half of businesses cite a shortage of graduates as an issue in their ability to recruit talent. Collectively, the industrial partners directly involved in the co-creation of the proposal have identified recruitment needs over the next decade that already significantly exceed the output of the CDT cohort.
Life science industries
The cohort will make a vital contribution to the UK life sciences industry, filling the skills gap in this vital part of the economy and providing a talented workforce, able to instantly focus on industry relevant challenges. Through co-creation, industrial partners have shaped the training of future employees. Additional experience in management and entrepreneurship, as well as peer-to-peer activities and the beginning of a professional network provided by the cohort programme will enable graduates to become future leaders. Through direct involvement in the CDT and an ongoing programme of dissemination, stakeholders will benefit from the research and continue to contribute to its evolution. Instrument manufacturers will gain new applications for their technologies, pharmaceutical and biotech companies will gain new opportunities for drug discovery projects through new insight into disease and new methods and techniques.
Health and Society
Research outputs will ultimately benefit healthcare providers and patients in relevant areas, such as cancer, ageing and infection. Pathways to such impact are provided by involvement of industrial partners specialising in translational research and enabling networks such as the Northern Health Science Alliance, the First for Pharma group and the NHS, who will all be partners. Moreover, graduates of the CDT will provide future healthcare solutions throughout their careers in pharmaceuticals, biotechnology, contract research industries and academia.
UK economy
The cohort will contribute to growth in the life sciences industry, providing innovations that will be the vehicle for economic growth. Nationally, the Life Sciences Industrial Strategy Health Advanced Research Programme seeks to create two entirely new industries in the field over the next ten years. Regionally, medicines research is a central tenet of the Northern Powerhouse Strategy. The CDT will create new opportunities for the local life sciences sector, Inspiration for these new industries will come from researchers with an insight into both molecular and life sciences as evidenced by notable successes in the recent past. For example, the advent of Antibody Drug Conjugates and Proteolysis Targeting Chimeras arose from interdisciplinary research in this area, predominantly in the USA and have led to significant wealth and job creation. Providing a cohort of insightful, innovative and entrepreneurial scientists will help to ensure the UK remains at the forefront of future developments, in line with the aim of the Industrial Strategy of building a country confident, outward looking and fit for the future.
Institutions
Both host institutions will benefit hugely from hosting the CDT. The enhancement to the research culture provided by the presence of a diverse and international cohort of talented students will be beneficial to all researchers allied to the theme areas of the programme, who will also benefit from attending many of the scientific and networking events. The programme will further strengthen the existing scientific and cultural links between Newcastle and Durham and will provide a vehicle for new collaborative research.