Prof S. Gadola: Structure-Activity relationships for CD1c-lipid binding BB/J017302/1

Lipids consist of water-insoluble hydrocarbon chains (HC). To fulfil their diverse and often vital roles in aqueous environments lipids partner with lipid-binding proteins. These proteins accommodate the water insoluble HC of lipids in deep hydrophobic channels, thereby shielding the HC from water. This type of interaction of HC with lipid-binding proteins is of crucial importance for diverse biological processes. New insights into the rules which govern protein-HC interactions will enhance our understanding of these processes and guide the development of new therapies. A prototypical example for a HC-binding protein is human CD1d, which exerts key roles in the body's immune system. The proposed research will use this protein as a model system to provide a systematic study into protein-HC interactions. In particular, it will examine how selective chemical modifications in a given model HC affect binding to CD1d. The twisted hydrophobic channels in CD1d and many other lipid-binding proteins inflict energetically unfavourable conformations on bound HCs. This mismatch between the shape of the lipid-binding protein channel and the preferred minimum energy conformation of the HC can be accentuated or neutralised by chemical modifications of the HC. We will employ fluorine atom modification of HCs which can exert a strong impact on HC conformation, while leaving the flexibility of the HC fully intact. The overarching objective of the proposed research is to provide a framework for the rationalisation of chemical HC modifications to manipulate their interaction with lipid-binding proteins. This may eventually lead to the development of new HC-containing drugs. The project embraces a cross-disciplinary approach employing sophisticated computational, synthetic and molecular biology techniques to achieve the following objectives: 1) To analyse the stabilising and destabilising effects of selective fluorine atom modifications on CD1d protein binding of a model HC. The HC-containing CD1d-binding antigen KRN7000, which is currently examined as a possible new drug in human clinical trials, will be used as a template for these fluorine modified HCs. Fluorine atom-modified KRN7000 analogues will be generated by chemical synthesis. The novel compounds will then be compared for their ability to bind and stabilise CD1d protein, and to switch on the immune function of CD1d. 2) In theory, a large number of fluorine-atom modified KRN7000 analogues could be compared. However, chemical synthesis of so many different lipids is not feasible. Therefore, we will employ high-end computational methods integrating empirical force fields and quantum mechanical calculations to guide the synthesis of a limited number of chemical KRN7000 analogues. 3) We expect that integration of the real-life CD1d-HC binding data from this project and the computational data will enable a deeper understanding of the mechanistic basis for the observed effects of fluorine-HC modifications on CD1d protein binding. This would be an important step towards rationalisation of protein-HC interactions and the development of a future computational modelling platform for HC-based drug design. The data generated in the proposed project will benefit different groups of academics, in particular: researchers working on protein-binding lipids; immunologists working on lipid-specific immune responses; synthetic chemists with interests in fluorine chemistry or glycolipid chemistry; computational chemists interested in complex systems modelling. If successful, the results of the proposed research will be of great interest for the pharmaceutical industry. KRN7000 and certain analogues of KRN7000 are currently being tested in human clinical trials. The proposed research may lead to rational design of novel KRN7000-derived analogues with therapeutic properties.