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Computer Modeling of Enzyme Catalysis and Inhibition
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Computer modeling techniques have been extensively §used to aid drug design via enzymatic reaction §studies. Here we present the investigations of the §catalysis by orotidine monophosphate decarboxylase §(ODCase) and the inhibition of protein kinase C §(PKC) isozymes. Decarboxylation, pseudohydrolysis §and covalent inhibition reactions were studied using §QM and QM/MM methods to understand the mechanistic §details of ODCase catalysis. The catalytic site §architecture and binding interactions of PKC §isozymes , and were also investigated in the §context of PKC- inhibitor, ruboxistaurin. Homology §modeling and docking techniques were used to model §the three-dimensional structures of the kinase §domains of PKC isozymes and the PKC-ruboxistaurin §complexes. For the first time, specific interactions §for ruboxistaurin that favor binding to PKC- were §uncovered. Our study provides opportunity to design §isozyme-specific inhibitors for PKC.
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