Synthetic Biology Applications of a New Generation of Antibody Catalysts

The use of antibodies as catalysts has long been the topic of research and discussion but initial attempts to utilise the concept in useful therapeutic or industrial settings has so far proved disappointing [1]. Significantly reduced catalytic rates in comparison to traditional enzyme catalysts remains the key reason for this lack of progress but recent technological developments that have launched a new generation of antibody formats and their use in "imprinting" enzyme catalytic sites [2] suggest that this topic is now worth revisiting. The VHH antibody format, for example, is capable of maintaining functional activity within a cell and can be expressed at high concentrations, which highlights its potential for overcoming any intrinsic low catalytic rate under specific circumstances. In particular, they may find use in catalysing useful synthetic process within engineered microorganisms when it is impractical or impossible to do this with an enzyme. It is also possible to envisage the use of libraries of intracellular antibody catalysts to generate libraries of natural product-like chemical compounds for use in inhibitor screening against pharmaceutically-relevant targets. Catalytic antibodies may also find therapeutic utility in degrading aggregated or misfolded protein in diseases such as Alzheimer's Disease [3].
This BBSRC-sponsored PhD study proposal will utilise the synthetic biology expertise at SYNBIOCHEM (Manchester Institute of Biotechnology) and the antibody format expertise and libraries at UCB to investigate this novel area of research and lay the groundwork for the future synthetic biology uses of catalytic antibodies. The work will be divided into three main areas of research:
1. The use of non-proprietary UCB antibody phage libraries to identify catalytic antibodies in reactions of particular interest to SYNBIOCHEM and where they already possess protein and crystal structures that could be used in the imprinting process. Early targets will be centred on conformational catalysis in driving the synthesis of different monoterpenoid scaffolds from geranyl diphosphate. In the second phase of the work we will target enzyme activities from enzymes that are known not to express functionally in E. coli. A good example is progesterone 5B-reductase, which belongs to the short-chain dehydrogenase/reductase (SDR) superfamily, and has been considered a key enzyme in cardenolide biosynthesis since it is the first stereospecific enzyme of the pathway leading to 5B-configured intermediates. Both these enzyme classes are major targets for metabolic engineering. Importantly, the second phase study will establish alternative routes to catalytic modules/parts based on antibody technology, for which expression of the natural enzyme is not possible in standard expression hosts such as E. coli.
2. The intracellular expression in microorganisms of VHH catalytic antibodies to test if they can be used for synthetic biology purposes in the production of novel chemical products
3. A detailed analysis of the potential to use catalytic antibodies to generate libraries of useful small molecules based on the chemically diverse monoterpenoid scaffold for use in generating "hits" against a therapeutically relevant target (to be defined by UCB).
We envisage that a 6 month placement at UCB will be essential for the student to gain knowledge in the use and application of our antibody libraries and their intracellular expression.