The Inhibitor Design Based On 4-hydroxyphenylpyruvate Dioxygenase

4-hydroxyphenylpyruvate dioxygenase(HPPD) is a class of non-heme Fe(II) oxygenase enzymes, which exists in a variety of organisms. At the end of twentieth century, HPPD is studied as a new target for new herbicide. Based on the different biomechanism, the HPPD inhibitors were designed and synthesized. In plants, HPPD catalyzes the conversion of 4-hydroxyphenylpyruvate(4-HPP) to homogentisate(2,5-dihydroxyphenylacetate, HGA).HPPD is a key enzyme in the pathway leading to production of plasoquinone and tocopherol from homogentisate, both essential cofactors in the photosynthesis cascade. In humans, HPPD is one of key enzymes in the tyrosine catabolic pathway. By the suppression of the formation of important cofactors, the photosynthesis process is interrupted. Inhibition of HPPD can lead to bleaching followed by necrosis and death.The triketone herbicides have good herbicidal activity. The triketone herbicides can combine with Fe2+in the active site of HPPD, which stops catalyzing the conversion of 4-hydroxyphenylpyruvate to homogentisate. As a result, the inhibitors of HPPD can disturb the biosynthetic material and kill weeds. HPPD inhibitors are one of high effective herbicides. It can be used by the pre-emergence and the post-emergence. They are nontoxic to animals and highly selective, environmentally benign. 4-hydroxyphenylpyruvate dioxygenase is an ideal target enzyme in the development of new herbicides.As the amino acids nearby the active site of HPPD play an important role in the interaction of the binding process between receptor and ligand, we simulate the protein receptor by constructing a protein model(PM) consist of the key amino acids near active site.The interaction energy between HPPD and ligands were calculated by the combination of simplified PM and density functional theory(DFT) method. The quantum mechanical interaction energies between HPPD and the 12 ligands provided by BASF company were estimated. We found the result from protein model combined with theory of DFT method shows a good linear relationship between the calculated binding energies and the experimental binding free energy with the correlation R=0.65. To make a comparison betweenDFT method and molecular mechanics method, we use molecular mechanics method(Autodock4.2.5) to calculate the binding energy between the same 12 ligands and HPPD,which shows wrong docking conformation can be obtained for ligands with nitro and amine groups using Autodock4.2.5 program. Autodock4.2.5 was further used for virtual screening from the part of ZINC database. By the analysis of the docking confirmation of high ranked ligands with high affinity, we found the docking conformations were much different from the experimental conformations, the compounds contain nitro, carboxyl or amino groups. With the comparison of the results from the molecular mechanics method and the protein model based on quantum mechanics method, the quantum-mechanical method based on PM and DFT is more reliable in affinity prediction for HPPD, which can be further used to design new HPPD inhibitors.Triketone herbicides are a major inhibitors of HPPD. We used the protein model(PM)and DFT method to study the interaction between HPPD and triketones such as NTBC([2-(2-nitro-4-three fluorine methyl benzoyl)-1,3-Cyclohexanedione]) and other 10 ligands. It shows there is a good linear relationship between the calculated binding energies and the experimental binding free energy with the correlation R=0.64. Finally, 4 compounds were designed based on the structure of NTBC. The designed HPPD inhibitors can be helpful for the environmentalist to develop new HPPD herbicides.