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J Comput Aided Mol Des ; 17(9): 567-81, 2003 Sep.
Article in English | MEDLINE | ID: mdl-14713189

ABSTRACT

We have developed a computational approach in which an inhibitor's strength is determined from its interaction energy with a limited set of amino acid residues of the inhibited protein. We applied this method to HIV protease. The method uses a consensus structure built from X-ray crystallographic data. All inhibitors are docked into the consensus structure. Given that not every ligand-protein interaction causes inhibition, we implemented a genetic algorithm to determine the relevant set of residues. The algorithm optimizes the q2 between the sum of interaction energies and the observed inhibition constants. The best possible predictive model resulting has a q2 of 0.63. External validation by examining the predictivity for compounds not used in derivation of the model leads to a prediction accuracy between 0.9 and 1.5 log10 unit. Out of 198 residues in the whole protein, the best internally predictive model defines a subset of 20 residues and the best externally predictive model one of 9 residues. These residues are distributed over the subsites of the enzyme. This approach provides insight in which interactions are important for inhibiting HIV protease and it allows for quantitative prediction of inhibitor strength.


Subject(s)
HIV Protease Inhibitors/chemistry , HIV Protease Inhibitors/pharmacology , HIV Protease/chemistry , HIV Protease/metabolism , Amino Acids/chemistry , Crystallography, X-Ray , Drug Design , HIV Protease Inhibitors/chemical synthesis , Kinetics , Models, Molecular , Models, Theoretical , Molecular Conformation , Protein Conformation , Reproducibility of Results , Structure-Activity Relationship , Substrate Specificity
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