Design And Structure-activity Relationship Of New Protoporphyrinogen Oxidase Inhibitors

The requirement for better living environment have largely increased since the new century, we realized that sustainable development can only be realized though harmoniously living with the nature, "green" have become one of the most famous word for the new century. Pesticides, as a special kind of chemical product, have brought many problems related to environment and health besides its contribution to agriculture, and discover of new green pesticide have became an important task faced by human beings. Compared with old pesticides, green pesticides have the advantages of high bioactivity, high selectivity, high safety and low residual, the key point of its discovery is to seeking of new leads with high bioactivity and high selectivity. Development of structural biology computational chemistry have resulted in the rapid development of computational aid drug design (CADD) method. Guiding the molecular designing with CADD method have become a potential strategies for new pesticide discovery.Protoporphyrinogen oxidase (PPO), the key enzyme in chlorophylls and haemachrome biosynthesis, has been identified as an important target for herbicides as well as new drugs. PPO herbicides get wide attention because their excellent properties, but more work is needed to fight against some drawbacks of this kind of herbicides. Design new inhibitors target at this important target based on CADD method is the main theme of this thesis.Structure and activity relationship of old inhibitors are important for designing of new compounds. In chapter Ⅱ of this thesis, based on the crystal structure of hPPO and mtPPO, we performed SAR study for two important series of PPO inhibitors based on a protocol containing docking, MM_PBSA calculation and SAR analyses. The binding modes of these inhibitors were validated by the high correlation between experimental bioactivities and the calculated data, we then discussed the SAR of these inhibitors based on the binding modes we got. In the second part of chapter II,3D-QSAR study were performed for three series of PPO inhibitors based on a new method containing molecular align method and CoMFA theory, which highlight the importance of substitute of these compounds for the interaction with the enzyme and the overall bioactivities of these compounds. The high-quality 3D-QSAR model we got can be used to guide the design of new compounds.Improving the selectivity is as important as improving the bioactivity when design new PPO inhibitors. In chapter III of this thesis, after comparing the binding pocket of hPPO and mtPPO we put forward a new hypothesis that the selectivity of some famous PPO inhibitors may resulted from the differences of these two structure. We then performed more study to validate our hypothesis, the binding of some commercial inhibitors of PPO was carefully discussed with the help of molecular modeling. We designed some new compounds based on fragment combination and virtual screening based substitute optimization, these new compounds show high activity and selectivity at the same time and show selectivity higher than 2000 for one of the compound. The result of the experimental study confirmed the validity of our mechanism and the advantages of our new approach.Hit-to-lead optimization if the key step of developing new pesticide leads. In consideration of the disadvantages of traditional hit optimization method. We developed a new method named computational substitute optimization (CSO) method, which can be used to quickly predict whether we can improve the bioactivity of the hits though substitute in specified place of a hit structure, this method can be used to guide the process of hit-to-lead optimization. We applied this method to help the Hit-to-lead optimization of a cytochrome bcl complex inhibitor, the bioactivity we got show high correlation with the calculated data, which demonstrated the accuracy of CSO method. We finally get 7 compounds after filtering by pesticide-likeness criteria, compound 18, which shows higher bioactivity than commercial fungicide AZ in the following field test are discovered after sterilization test. Compound 18 is a potential lead for new fungicide and we found that our predicted binding mode of this compound is very close to the crystal structure, which demonstrate the reliability of CSO method.Seeking of new scaffold always bring new hope for the discovery of potential lead compounds. In the last part of this thesis, we tried to find new scaffold structure with high selectivity targeting at PPO though virtual screening with the guiding of the knowledge we get though the previous study. We designed a new screening strategy by considering both the special structure properties of PPO herbicides and the selectivity towards different species. Finally,25 new structures were obtain after filtering by consensus docking, MD study and MM-PBSA calculation. Most of these new compounds could form strong interaction with Phe392, R98, F353 and G175 in the binding site. Biological tests indicate that 23 compounds with the bioactivity in micro mole range and most of them show highly selectivity at the same time, which shows the success of our screening strategies. Our work is the first time to perform virtual screening of PPO inhibitor considering selectivity. Though this work, we got many new structures which deserved optimized on one hand, the new screening strategies is also helpful to the virtual screening of other targets at the same time.