Molecular Modeling Study On The Interaction Mechanisim Between The Neonicotinoid Insecticides And NAChR

The neonicotinoid insecticides acting as nicotinic acetylcholine receptors(nAChRs)agonist are used for crop protection and animal health globally.However,due to their widespread use,insecticide resistance has emerged.Therefore,to develop potent and effective neonicotinoid insecticide targeted on nAChR,uncovering the insecticide resistance mechanism to IMI at the atomic level is very urgent and important.Target-site mutations of nAChR have become one important resistance mechanism.However,molecular mechanism of insecticide resistance has not been elucidated.In this paper,computer-aided drug design methods such as molecular docking,molecular dynamics simulation,MM/GBSA calculation,PCA analysis and RIN analysis are mainly used.The first part of this thesis is to study the mechanism of Imidacloprid(IMI)resistance induced by nAChR mutations.Target-site mutations(Y151S and R81T)of nAChR are one important resistance mechanism to IMI in different insects.Due that the 3D-structure of the insect's nAChRs is still unknown,here Ls-AChBP was used,which sequence is similar to nAChR.From the sequence alignment,residue Y151 and residue R81 in nAChR are at the position analogous to residue H145 and Q55 respectively.Due that there is no the crystal structure of the complex between nAChRs and IMI,we used Ls-AChBP and its two mutations(H145S and Q55T)to investigate the IMI resistance mechanism.The value of binding free energy indicated that the interactions of the two mutations with IMI decreased.From the further free energy decomposition analysis,we found that the contribution of residues in the binding pocket altered.Additionally,the residue interaction network(RIN)analysis combined with PCA analysis revealed the two mutated residues both changed the conformation and residues' flexibility of IMI binding pocket,caused by the conformational change of the residues which had direct interactions with the mutated residues.These results can explain the reason why the studied mutations lead to resistance to IMI,and will be helpful to design more potent inhibitors which also work on the mutant.The second part of the thesis focuses on the mechanism that Sulfoxaflor and Dinotefuran have different effects on the R81 T mutanted nAChR.Sulfoxaflor and Dinotefuran were first docked into the receptor by molecular docking.The values of the calculated binding free energy were consistent with the rank of experimentally observed resistance levels.Combined with pocket volume calculation,it was found that the binding pocketin the complex of Ls-AChBP with Sulfoxaflor became smaller,which resulted in the binding between the ligand and the receptor more tight.So the binding ability of Sulfoxaflor to the binding pocket did not change when the mutation of R81 T occurred although the contribution of some direct interaction residues reduced.The Dinotefuran resistance is due to the conformation change of the binding pocket and further leading to the decrease of the binding free energy contribution of the residues W143,T144,Y185,A103 and L112.The third part of the paper is based on the conclusions of the second part that nAChR R81 T mutant has no resistance to Sulfoxaflor and we performed structure modification on Sulfoxaflor.The structure of Sulfoxaflor was modified by Schr?dinger software to develop potent and effective neonicotinoids against the wild type and insect variants.Firstly,we performed the structure-based design from the structure of Sulfoxaflor by Schr?dinger software.And then,the modified small molecules were evaluated by the technique of virtual screening,such as Lipinski rules and molecule docking protocols.Finally,43 top ranked molecules were reserved,and these small molecules had high binding affinity with wild type and Q55 T mutant Ls-AChBP according to MM/GBSA calculation.Our study not only explains the mechanism why Imidacloprid,Dinotefuran and Sulfoxaflor have different effects on insect variants,but also helps to design small molecule based on Sulfoxaflor.All theses results are helpful for the further development of more effective insecticides.