Dissertation
Dissertation > Agricultural Sciences > Plant Protection > Pest and Disease Control > Crop pests and diseases and their prevention > Cereal crop pests and diseases > Corn pests and diseases

The Virtual Screening of Chitin-Degrading Enzyme Inhibitors for Asian Corn Borer

Author ChenYangYan
Tutor ZhangHongYu
School Huazhong Agricultural University
Course Biochemistry and Molecular Biology
Keywords Specific Molecular Targets Endochitinase Exochitinase MolecularDocking Molecular Overlaying Substructure Search Superimposed HomologousProteins
CLC S435.13
Type Master's thesis
Year 2013
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The development of insect larvae into adults involves a characteristic process, namely molting metamorphosis, during which large amounts of chitin is synthesized or degraded. Therefore, chitinases (endochitinases and β-N-acetyl-D-hexosaminidase), playing a major role in chitin degradation, are considered as potential targets for green pesticides. Based on the information on the crystal structures of chitinases, we sought to employ computer-assisted drug design methods to find out small molecules of high activities against them, and to guide the research and development of new highly effective, specific and safe pesticides.As to corn borer exochitinase, we had the crystal structures of β-N-acetyl-D-hexosa-minidase in complex with three inhibitors respectively, namely TMG-chitotriomycin, PUGNAc and NGT:(1) We applied receptor structure-based virtual screening approach. We chose ZINC, SPECS, Enamine, MOE and May bridge as small molecule databases. Then three docking programs, namely GOLD, FlexX and Vina were in turn used to screen for active chemicals. Then after further analyzing the results, we obtained and purchased several chemicals that had relatively good binding poses, and subsequently examined their inhibitory activities by experiment. Through the screening, we found two small molecules from SPECS that had high inhibitory activities when inhibitor concentration was250μmol/L. One was AK-968/11987282, with64%inhibitory activity. The other one was AL-281/40711501, and the inhibitory activity was54%;(2) Ligand structure-based molecular overlaying method was also used. We chose the most representative ligand PUGNAc as template and employed Surflex-sim to perform molecular overlaying to get the similar molecules.As to endochitinase, we had the crystal structure without ligand:(1) The homologous proteins superposing method could be used to speculate the binding site of the known crystal structure;(2) Additionally, endochitinase and exochitinase have similar structures and catalyzing mechanisms, so we verified the activity against endochitinase of purchased compounds. Then five compounds from Enamine were found to be able to inhibit endochitinase. Through analyzing the five chemicals, we uncovered that they possessed a common substructure. Accordingly, substructure search was employed to find out chemicals of higher inhibitory potency. We utilized Pipeline Pilot to conduct substructure search against TOPSCIENCE and ZINC, selectively purchased the compounds we got, and then the inhibitory activities were tested. Finally we found one small molecule had relatively high inhibitory activity.

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