At present, there are many co-crystal structures of antigen and antibody in the PDB database, and some antibodies have been proven to be used for the inhibition of molecular functions. I have seen that many drug designs or screenings introduced in the literature use ligand-receptor binding sites, but I have not found any direct use of the crystal structure information of antigen-antibody binding to design small-molecule drugs. Has anyone tried or thought about it?
The main problem with using antibodies recognising a particular epitope as a template for designing small molecules interacting with the same target lies in the fact that antibodies frequently recognise either loops sticking out from the target molecules or flatish surfaces (typical protein-protein interfaces). They rarely bind to the type of pockets and crevices that are optimal targets for small molecules.
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