The Rational Design, Synthesis And Bioactivity Of Structure-based Novel Protoporphyrinogen Oxidase Inhibitors

Development and research of novel pesticide is a very complex project. Moreover, discovering and optimizing the lead structure is the key bottleneck for this project. Accelerating the speed of discovering and optimizing the lead structure can shorten the periods of developing novel pesticide. In recent years, computer-aided drug design, combinatorial chemistry, enzyme screening and high throughout screening methods are widely used to design novel pesticide and quickly increase in the level and speed of developing novel pesticide. The screening and design based on the interaction of enzyme and inhibitors is a timesaving and high effective way and can accelerate to design and synthesize some potential and effective inhibitors.The herbicides of inhibiting photosynthesis are widely studied in the herbicide research. Because photosynthesis is an own physiological process for the advanced green plant, while in animals this character doesn't exit. Herbicide-bleaching is widely studied among the photosynthesis herbicides and can inhibit the formation of chlorophyll. Protoporphyrinogen oxidase (Protox, EC 1.3.3.4), the key enzyme in chlorophylls and haemachrome biosynthesis, has been identified as the important target site of action for several herbicides. For the decade, protoporphyrinogen oxidase inhibitors in the new hebicides are frequently reported. These herbicides have the following characteristics: Based on the chloroplast in the cell of plants, having the high selectivity between plants and animals. Because the inhibitors mimic the partial characteristics of the substrate protoporphyrinogen IX and compete to combine the active site of Protox, and resistance to the inhibitors can't be created in the weed. And low application rates, low residue and environmetal safety. So we use the computer-aided drug method to design new protoporphyrinogen oxidase inhibitors and synthesize these compounds based on the current Protox inhibitors and Protox crystal structure from tobacco.Firstly, DFT/2D-QSAR and DFT/3D-QSAR based on the structures of phenyl triazolinones and cyclic imides were studied for the first time. And we connect the density functional theory with QASR study and analyse the relationships between the electrostatic properties, hydrophobic properties, steric properties and the structures for these compounds. Based on these study, we build a ligand model. In additional, we use the DFT/QSAR model to choose the active conformation for flexible molecules, and validate this model with molecular docking, molecular dynamic and the potential surface scanning, give a new method to select the active conformation for flexible molecules when the crystal structures of the receptors are unknown.Secondly, we discuss the interaction ways between protoporphyrinogen IX and protoporphyrinogen oxidase, between cyclic imides and protoporphyrinogen oxidase, between phenyl traizaolinones and protoporphyrinogen oxidase using the molecular docking, molecular dynamics methods, based on the crystal structure of protoporphyrinogen oxidase from tobacco. And we find a new amino acid Glyl75 has an important effect on the substrate and inhibitors, except for some conservative residues reported from the literature. Based on these study, we build the receptor model and use it for the virtual screening study.Thirdly, Maybridge database is employed for the primary screening based on the ligand model and receptor model built from our study. Scoring functions based on Dock, FlexX, Cscore are used and 33 candidate molecules are found. These compounds will be test for herbicidal and inhibitory activity.Lastly, on the base of the ligand model built from DFT/QSAR study, we modify the structure for current inhibitors and design novel protoporphyrinogen oxidase inhibitors. Moreover, 14 compounds were synthesized and will be test for herbicidal activity. The activity result shows that some of this kind of compounds has good herbicidal activity.