Theoretical Study On The Structure-Function Relationship Of HPPD And Computer-Aided Design Of HPPD Inhibitors

4-hydroxyphenylpyruvate dioxygenase (HPPD) is a non-heme Fe(II)-dependent enzyme involved in the metabolism of tyrosine in most organisms and in the biosynthesis of tocopherols in plants. Potential HPPD inhibitors provide an alternative strategy for treating the life-threatening tyrosinaemia type I disease, and several of them, including mesotrione, sulcotrione, and isofluxatole, are currently in use as selective broad leaf herbicides. The thesis is designed mainly to explore the structure-function relationship of HPPD and design new HPPD inhibitors. It content include homology modeling, molecular docking and quantitative structure-activity relationship, which can be divided into three parts as follows:The first part is about the homology modeling of p-hydroxymandelate synthase (HMS). HPPD and HMS are high homology and share the same substrate, p-hydroxyphenylpyruvate (HPP). However, their catalytic functions are of much difference. Using HPPD as a structural template, the 3D structure of HMS was built with homology modeling method. Rational analysis of the modeled structure was performed. To validate the applicability of AutoDock to the non-heme iron dioxygenases, molecular docking of HPPD with the inhibitor, 2-nitro-4-(triflouromethyl)benzoyl]-1,3-cyclohexanedione (NTBC), was carried out, and the effects of three different forms of NTBC and the bearing charge of the metal ion upon the docking results were evaluated. Subsequently, docking calculations of HPPD and HMS with the substrate HPP were conducted. A comparison of the binding mode of these two enzymes with HPP was made. While the three residues that coordinate to the Fe²⁺, His, His and Glu, are important for the tight binding of both enzymes with the substrate, the conserved residues near the substrate, Leu228, Pro243, Asn245 and Phe364 in HPPD (1T47) and Met187, Thr202 and Ile204 in HMS, play a crucial role in determination of the reaction pathway. This may provide a start point for the understanding of their difference in catalytic function.In the second part, we focus on the quantitative structure-activity relationship (QSAR) of HPPD inhibitors. Conventional 2D-QSAR method using mostly the molecular connectivity index as structural descriptors, and the hologram QSAR (HQSAR) were adopted. For the HQSAR model, satisfying results were obtained with cross-validation coefficient (q²) and linear correlation coefficient (r²) equal to 0.815 and 0.930, respectively. These models will provide a useful guide for synthesizing new HPPD inhibitors.In the third part, the study was design to examine the effect of tautomerism upon the CoMFA results. Three selected data sets involving protropic tautomerism, which are HPPD inhibitors, inhibitors of puromycin-sensitive aminopeptidase (PSA) and anxiolytic agents, were used for this purpose. As tautomeric forms of a molecule exhibit difference in functional groups, it might expect that they have different electrostatic and steric field distributions, at least around the involved functional groups, and therefore affect the field-based 3D-QSAR results. All-orientation and all-placement search (AOS-APS) based CoMFA models, in addition to the conventional ones, were derived for each system and proved to be capable of yielding much improved statistical results. The results indicate the importance of selecting proper tautomer in the CoMFA studies. Furthermore, there existed some substantial differences of the electrostatic field contours between the two different tautomeric forms for all of the three systems considered, whereas the differences in the steric field contour maps were limited. This implies that the resulting new potent ligands may be quite different if one utilizes the CoMFA models of different tautomeric forms for guiding further structural refinements. The traditional 3D-QSAR was applied to investigate the tautomer of the molecule and try to predict the active structure of inhibitor which is the brand-new expansion of the traditional method.