Potential Targets Screening Of Steroids Based On Molecular Simulation

Steroids are widely found in organisms,which involved in regulating life processes,having great significance in theoretical research and practical applications.At present,the research on steroids function has extended to the molecular level,but there are still many problems to be solved,such as the molecular mechanism of the biological activity of steroids,and the side or multi-effects of steroid drugs.Identifying potential targets of steroids is of great significance in studying the above issues.Systematic screening of targets is of great cost by traditional experimental methods,while using molecular simulation methods to virtually screen potential targets can get rid of the blindness of targeting,reduce the range of candidate proteins for molecular experiments and improve the screening efficiency.Although there are already some online small molecule target prediction tools,the prediction results cannot provide a valuable reference due to low precision,long period,and high false positives.To predict the targets with more accuracy,we constructed a specific target library for the prediction of steroids targets by reverse docking,and selected two types of steroid molecules for prediction accuracy evaluation and target pre diction research.The major results are as follows:(1)A steroids-specific target library integrating 3325 PDB or homology modeling structures was built by considering chemical similarity from DrugBank and biological processes from KEGG.And the crystal structure is divided into 196 categories according to its protein type,which improves the effectiveness of the ranking of prediction results.Functional analysis of the protein of the candidate target library revealed that they are mainly binding proteins and catalytic related enzyme proteins.Structural redundancy analysis of each type of protein indicated that sixty of the proteins contained more than five crystals,and these redundant crystal conformations took the flexibility of the protein into account in subsequent reverse docking predictions.(2)The reverse molecular docking method is used to predict the target of glycocholic acid from the target library to examined the coverage and prediction accuracy of the target library.There are 7 known targets for glycocholic acid,three have no crystal structure and no homologous sequences,and protein-based prediction methods cannot predict these three targets due to their own limitations.the other remaining 4 crystallographic targets can be successfully predicted,and the ranking is in the top 40,compared to idTarget,one of the prediction tools online,only giving two targets with bad ranking at 615 and 2583 respectively,our target library exhibited wondering targets coverage and effective accuracy.And the binding mode of glycocholic acid and three of the targets(FXR,VDR,GT)coincided with the original ligand's orientation at the active site,and shared with the same amino acid residues involved in hydrogen bond formation.Due to the great difference of binding mode between another target of glycocholic acid molecule(NXR)and the initial ligand,we further studied the dynamic stability of its binding mode.The root mean square difference(RMSD)is stable at 2 angstroms indicated that the conformation of the composite structure is relatively stable during the binding process.(3)Among the predicted potential targets for 24-epi by this method,the known target BRI1-BAK complexes in plants ranked first in the prediction results,indicating that the prediction results were relatively accurate.Except for the remarkably BRI1-BAK target,five kinds of disease related proteins were selected from the top ten percent of the results for binding mode analyzing.Then two types of proteins with strong binding ability,P450 family and G-coupled receptor,were determined to make further dynamic stability evaluation.It was found that the RMSD of complex backbone was pacing within 2 angstroms.For the transmembrane region of SMO protein is relatively conservative,and where the binding site of EBR located near the outer side in the transmembrane region,on account of the initial ligand is an anti-cancer molecule able to induce conformational changes during the binding process consistent with the larger structural changes in the complex,it is speculated that the SMO protein is very likely to be an anticancer target for 24-epibrassinolide.