MOLECULAR ELECTROSTATIC POTENTIAL ANALYSIS FOR ENZYMATIC SUBSTRATES, COMPETITIVE INHIBITORS, AND TRANSITION-STATE INHIBITORS

Recent advances in the application of kinetic isotope effects to enzym e-catalyzed reactions have provided reliable information for enzymatic transition state structures, A method is presented for quantifying th e similarity of substrates and inhibitors with their enzyme-stabilized transition states. On the basis of transition-state stabilization the ory for enzymatic reactions, molecules most similar to the transition state structure bind with greatest affinity, Molecular similarity meas ures are applied to compare substrates, competitive inhibitors, and tr ansition state inhibitors with the transition state structures stabili zed by the enzymes AMP deaminase, adenosine deaminase, and AMP nucleos idase. (R)- and (S)-Coformycin 5'-phosphate are inhibitors for AMP dea minase, with the R-species superior to its enantiomer. Formycin 5'-pho sphate 4-aminopyrazolo [3,4-d] pyrimidine-1-ribonucleotide, and tuberc idin 5'-phosphate inhibit AMP nucleosidase. The transition state for a denosine deaminase is analogous to that for AMP deaminase, allowing an alysis of the tight-binding hydrate of purine ribonucleoside and of a weaker inhibitor, 1,6-dihydropurine ribonucleoside. The basis for rank ing molecules for similarity to the transition state is the distributi on of electrostatic potential at the molecular van der Waals surface. Spatial properties of a molecule are described through the topography of the surface, while the electrostatics capture ionic, hydrogen-bondi ng, and hydrophobic features. A test molecule is compared with the tra nsition state by orienting the two species so that their van der Waals surfaces are maximally coincident. At this orientation, a single meas ure sensitive both to the electrostatic potential and its spatial dist ribution is used to rank the electronic similarity. For AMP deaminase, adenosine deaminase, and AMP nucleosidase, the transition state inhib itors are quantitatively more similar to the transition states than ar e the substrates. A strong correlation between the binding free energi es and the similarity measures is found for most of the transition-sta te inhibitors in all three enzyme systems. This method is useful in th e logical design of transition state inhibitors and may be applied to similarity searches of chemical libraries.