chapter  L4
5 Pages

Modeling Studies

WithGraham Patrick

The protein-inhibitor complex can be fed into a computer and molecular modeling software can be used to study how the inhibitor is bound to the active site. Molecular modeling studies made it possible to identify the binding interactions. Using molecular modeling, adenosine triphosphate (ATP) was removed from the binding site and CGP52411 was fitted into the binding site in its place, then docked in order to get the strongest binding interactions. The design of enzyme inhibitors is made easier if the shape and format of the enzyme’s active site is known. Ideally, this involves crystallizing the enzyme with an inhibitor bound to the active site then carrying out an X-ray crystallographic analysis. The bidentate binding interaction observed for the pyrimidine ring of ATP is mimicked by the imide moiety of CGP52411, where NH acts as a hydrogen bond donor and a carbonyl oxygen acts as a hydrogen bond acceptor.