Virtual Screening And Molecular Docking Of 1-deoxy-d-xylulose 5-Phosphate Reductoisomerase Inhibitors

ObjectiveThis topic combines the method of computer aided drug design(CADD).Crystal structure analysis of DXR enzyme,1Q0Q in the PDB database,is used by the method of molecular composite 1Q0Q structure model for the structure of virtual screening and the complexes of magnesium is regarded as a foundation.To determine a target area,the size of about 234 atoms through virtual screening method are combined with biological activity evaluation.Finally,we selected 149 compounds.The molecular docking method was used to dock the compound with DXR enzyme,and the binding mode of the compound and DXR enzyme was determined.It is hoped that experimental verification at the cell level will be carried out in the later stage,and their inhibitory effect may be improved through modification and optimization,so as to obtain new antibiotics.Methods1.Analyze the crystal structure of DXR downloaded from the PDB database,and select 1Q0Q crystal as the main structure.By means of molecular superposition,based on the coordinate positions of amino acids D150,E152,S186,H209,E231.hydroxy acid reductoisomerase(2EGH)and DXR(1Q0Q)are superimposed,and the Mg2+in 2EGH is retained at 1Q0Q as a follow-up the structural basis of small molecule screening.After protonation and structural optimization of the crystal,the binding domain of 1Q0Q is analyzed to find the most suitable target binding region2.Use the virtual screening software FRED(Ver 3.2.0.2)to screen the pockets,and screen them step by step in the Chemdiv database,IBS natural product library and TargetMol compound library.Then score based on the affinity value and other attributes(pharmacological properties,water solubility,drug metabolism,cardiotoxicity),use protein ligand interface fingerprint(PLIF)method to analyze the interaction sites and force types between them and DXR targets,and comprehensively analyze and select potential inhibitors based on the background of traditional Chinese medicine.3.After conducting a background study on the compound,the software FRED(Ver 3.2.0.2)is used for molecular docking of the compound with the pre-processed structure,and then the MOE software is used for mapping to explore the binding mode and analyze the inhibition mechanism.4.The enzyme inhibitory activity and inhibitory concentration(MIC)of the candidate compounds were determined to verify the results of virtual screening.Results1.Determine the basis of the best crystal structure,determine the target binding domain of about 234 atoms,reveal the active pocket of DXR inhibitor and the hot amino acids related to the high activity and selectivity of the ligand,for later virtual screening and molecular docking.2.Select 149 potential inhibitors according to the combination of empirical judgment,activity determination,pharmacokinetic,toxicity assessment and other characteristics.Select six compounds:Rhamnetin,Okanin,2’,3,4,4’,6 ’-5 hydroxy chalcone,Urolithin M6,2hydroxy-3-(hydroxymethyl)anthraquinone and salvianolic acid C3.The molecular docking technology was used to study the binding mechanism of 6 compounds with DXR enzyme at the molecular level;the correlation effect formed in the active pocket was explained,and theoretical guidance was provided for the structural optimization of potential inhibitors in the later stage.4.Rhamnetin and urolitin M6 had a certain antibacterial effect on Escherichia coli,Pseudomonas aeruginosa and Methicillin-resistant Staphylococcus.Salvianolic acid C had a certain antibacterial effect on Escherichia coli.ConclusionAfter virtual screening of DXR enzyme,we explored in detail the six potential DXR inhibitors and the inhibition mechanism of DXR enzyme,and carried out experimental verification.We hope to obtain new antibiotics with better antibacterial efect through structural optimization and modification on this basis in the later stage.