MAST, Modular Activator and Silencer Therapeutics

The human body produces antibodies that recognize antigens on unwanted invaders such as bacteria and viruses. These antibodies then help direct the immune system against the invaders to destroy them. Antibodies can do this because there are millions of variations of them and each one has a unique specificity for a particular target, e.g., a particular type of antigen displayed only on one type of bacteria. This special property of antibodies has also allowed scientists to manipulate them to recognize many other useful targets of interest, for example in cancers, or to act as a marker to measure the amount of a product of interest in a scientific experiment. In fact, this has happened to such a degree that it is now unlikely any other type of protein has made a greater contribution to the advancement of biological research and the development of protein therapeutics than the humble antibody. It has been a participant in pretty much every biological engineering experiment conceivable. Even so, there remains huge potential for new antibody applications, and it is essential that the UK bioscience sector continues to be at the forefront of antibody technology development.

Here we propose to expand the potential of antibody technologies by developing three new antibody platforms, each of which gives antibodies a new and different ability. The first platform will give antibodies the ability to not only bind a target but also change its behaviour. There are many diseases that are caused by proteins being overactive or underactive, and consequently, being able to make antibodies that can correct the activity level in a target protein would be enormously therapeutically useful. Currently, antibodies that bind a target are generally discovered from libraries of antibodies of all sorts of different shapes. Instead, we will create a library that is biased towards antibody shapes that are more likely to be able to bind and change a target's behaviour. The second and third platforms will instead contain arrays of proteins with specialised functions to either send a target to be degraded by the waste-disposal machinery inside a cell (degraders), or to act like scissors to directly cut up and destroy the target (proteases). These arrays will be designed so that they can be linked to any antibody of choice. The antibody can then be used to direct these proteins to a specific target where they can degrade or destroy it. These platforms will be invaluable for tackling any disease where a particular protein is overactive and causing problems, as occurs in many cancers, and so degrading or destroying it is an ideal therapeutic approach.

For this project we have brought together a specialist team in protein engineering of antibodies, degraders, and proteases, with experience in artificial intelligence, structural biology, protein evolution, and pharmacological assay screening. To our knowledge there are no technology platforms currently available that fulfil the three purposes proposed here. We will make, test, and validate these platforms. Because all three platforms involve giving antibodies new abilities and they require overlapping methods for antibody production and screening it makes perfect sense to apply a team approach to developing these technologies together in parallel and employ a team of scientists with expertise in biochemistry or assay design, who can synergise workflows to ensure effective delivery of the project goals. We will then make the platforms available to UK academia and industry so that they can also use them. In addition, we have also engaged with industry partners to secure their support, including potentially aiding in screening of potential therapeutic leads. We believe that the creation of these technology platforms will facilitate the development of new antibody therapeutics and empower the UK bioscience sector.

We will create and validate three technology platforms each of which gives antibodies new and different properties for use as therapeutic agents. The first platform is a library of synthetic binders that are biased to modulate the function of a target by stabilizing a conformation rather than binding it neutrally (state stabilizers). To do this, we will identify nanobody structures in complex with folded antigens, where the complementarity determining region (CDR) 3 binds a pocket or cleft and is selective for stabilizing a state e.g. an activated ion channel. Guided by structural biology and artificial intelligence approaches we will design ten libraries against these nanobody blueprints and order them synthetically. Together they will create a versatile master library covering a wide range of state-stabilizer CDR arrangements. We will screen the library by phage display against suitable targets and test for functional effects in cell assays. This includes using electrophysiology to show modulation of ion channels and electron cryo-microscopy to show nanobody binding modes at pockets and/or crevices as thorough proof-of-concept. For the other two platforms we will design arrays of E3 ligase and protease modules capable of degrading or proteolytically cleaving targets. These will contain a SpyCatcher tag for pairing with any antibody of choice (that has a SpyTag). The antibody will therefore have gained the new ability to bind a specific target and degrade it, or to bind a specific target and destroy it. Each array will be conjugated to suitable antibodies and screened in cell assays in order to validate the actions of these arrays, and they will also be tested in a therapeutically relevant system e.g., on cancer cell lines. Overlapping methodologies are required to execute delivery of all three of these platforms and so a PDRA team will synergize different skillsets to ensure a successful outcome.