Evolution of Inhibitors

Inhibitors may also be generated by the use of molecular evolution. This technology has been successfully applied to thrombin [29]. In brief, a synthetic scheme is chosen that potentially enables the synthesis of a very large combinatorial library in this case, a three-component Ugi-type reaction was selected. A small set of molecules is synthesized with a random choice of components and tested 

A very informative practical exercise would be to use the approach with a number of synthetic schemes, to observe the binding modes of the best inhibitors by use of X-ray crystal structure determinations, and to superimpose the resulting structures. This would then enable a 3-D mapping of the active site on the assumption that inhibitor features occurring most frequently at a particular spatial location indicate the most favorable functional group to place at that point. Further, the range of relevant low-energy structures of the protein would also be mapped. 

The important principle here is that although a single ligand-protein complex contains much useful information, the overlay of a series of complexes - as independent of each other as possible - gives a much more objective picture of which interactions contribute most to affinity (and, in principle, to selectivity). 

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