The Study Of Dunhuang Mofeng Prescription On The Treatment Of Rheumatoid Arthritis Based On Network Pharmacology

Objective: To explore the action mechanism of Dunhuang Mofeng prescription based on network pharmacology,molecular docking technology,and molecular dynamics.Network pharmacology was used to screen the active components of Dunhuang Mofeng prescription,predict the therapeutic targets of Dunhuang Mofeng prescription,collect the targets of rheumatoid arthritis,construct the component-target-pathway network of Dunhuang Mofeng prescription to analyze its mechanism,screen the potential ligands of Dunhuang Mofeng prescription by molecular docking technology,and evaluate the binding ability of the potential receptor protein and the potential ligand.Molecular dynamics was used to simulate the conformational stability of the protein and ligand in the complex.Methods: The Dunhuang Mofeng prescription contains 7 Chinese herbs,such as aconite,salvia miltiorrhiza,Shu pepper,Chuanxiong,angelica dahurica,rhubarb,and croton.Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP)was used for data retrieval.The screening conditions were set according to the five rules of Lipinski,and the relative molecular mass(MW)was ≤500Da.Fat-water partition coefficient(Alog P)≤5;Hydrogen bond donor(Hdon)≤5;Hydrogen bond acceptor(Hacc)≤5;The chemical information database of Dunhuang Mofeng prescription was constructed.The potential targets of the selected active ingredients were searched in the TCMSP database,and then the target network of the active ingredients of the Dunhuang Mofeng prescription was constructed.Using "Rheumatoid Arthritis" as the key word,RA-related targets were searched in Gene Card,OMIM,Pharm Gkb,TTD,Drug Bank,and RA disease gene databases were collected.The information from the two databases was merged to obtain the intersection genes of Dunhuang Mofeng prescription targets and rheumatoid arthritis targets and to obtain the potential therapeutic targets of Dunhuang Mofeng prescription for RA.Furthermore,the function and pathway analysis,protein interaction analysis,GO and KEGG enrichment analysis of the targets were performed to construct the active ingredient-RA disease target network.Through the previous network pharmacology research,the active ingredients of traditional Chinese medicine that can be used in the treatment of rheumatoid arthritis were screened out.The 2D structure of small molecule ligands was downloaded from the Pub Chem database,and the 3D structure was transformed by Chem3D14.0.Auto Dock Tools1.5.7software was used to add full hydrogen to the ligand,set the ligand(automatically assign charge),detect the torsion bond,and set the torsion bond.PDB database was used to find the3 D structure of the receptor protein.Py MOL2.6.0 was used to dehydrate and de-ligate the receptor protein,and Auto Dock Tools1.5.7 was used to complete the H treatment.Auto Dock Tools1.5.7 was used for molecular docking,and the lowest binding energy was selected for export.Py MOL2.6.0 and Discovery studio2017.R2 were used for 3D and 2D visualization analysis of the docking results.GROMACS 2020.3 was used to simulate the molecular dynamics(MD)of the receptor-ligand complex with the lowest molecular docking binding energy.Excle2019 was used to visualize the data,and the IC50 and ADMET properties were predicted.Results:1.Network pharmacology analysis showed that 11 core active ingredients(quercetin,apigenin,luteolin,emodin,dihydrotanshinone Ⅰ,tanshinone B,cryptotanshinone,myristoone,aloe emodin,tanshinone A,isotanshinone I)in Dunhuang Mofeng prescription targeted 110 genes related to RA.110 genes were involved in the regulation of multiple signaling pathways,including the AGE-RAGE signaling pathway in diabetic complications,interleukin-17 signaling pathway,TNF signaling pathway,fluid shear stress and atherosclerosis signaling pathway,lipid,and atherosclerosis signaling pathway,etc.2.Molecular docking showed that cryptotanshinone,tanshinone A,tanshinone B,isotanshinone I,luteolin,quercetin,aloe-emodin,apigenin,and other active ingredients had a good binding activity with key target proteins such as STAT3,MAPK14,MAPK1,TNF,IL6.Among them,it had a better binding activity with the lowest score of MAPK14(<-7.0kcal/mol).These results indicate that the treatment of rheumatoid arthritis with the treatment of saphenone,tanshinone A,tanshinone B,isotanshinone I,luteolin,quercetin,aloe-emodin,and apigenin can target STAT3,MAPK14,MAPK1,TNF,IL6,and other proteins.3.The best molecular docking model was simulated by molecular dynamics,and the results showed that the root mean square fluctuation(RMSF)of the docking complex in the solvent system tended to fluctuate between 0.05-0.3nm,indicating that the protein and ligand in the docking complex had a stable conformation.4.Danshenxinkun B,the active ingredient in Dunhuang Mofeng prescription,was predicted by IC50 and ADMET.The IC50 prediction results showed that Danshenxinkun B had toxic effects on metastatic melanoma and other cell lines,and ADMET calculation showed that Danshenxinkun B had better drug formation.Conclusions:1.STAT3,MAPK14,MAPK1,TNF,and IL6 are the core target genes of Dunhuang Mofeng’s prescription for the potential treatment of rheumatoid arthritis.Quercetin,apigenin,luteolin,emodin,dihydrotanshinone Ⅰ,tanshinone B,cryptotanshinone,myristoone,aloe emodin,tanshinone A,isotanshinone I are the potential core active ingredients of Dunhuang Mofeng prescription.These 11 potential active ingredients may bind to the docking pockets of STAT3,MAPK14,MAPK1,TNF,IL6,and other target proteins.2.Dunhuang Mofeng prescription may be involved in cellular processes including cell proliferation,gene expression,differentiation,apoptosis,lipid metabolism,and coagulation,as well as osmotic stress,heat shock,and proinflammatory cytokines.It may be involved in the AGE-RAGE signaling pathway,IL-17 signaling pathway,TNF signaling pathway,PI3 KAkt signaling pathway,MAPK signaling pathway,and other related signaling pathways in diabetic complications to treat RA with multiple targets and multiple pathways,thereby affecting the process of rheumatoid arthritis.3.Dunhuang Mofeng’s prescription has a potential role in the treatment of rheumatoid arthritis by targeting inflammatory response or cell apoptosis signaling pathways to affect inflammatory response and bone metabolism through a multi-component,multi-target,and multi-pathway approach.4.The screening method based on network pharmacology,molecular docking,and molecular dynamics theory can be used to find the active ingredients and main targets of Dunhuang Mofeng prescription in the treatment of rheumatoid arthritis and provide some reference basis for further study of the mechanism of action of Dunhuang Mofeng prescription in the treatment of rheumatoid arthritis.Predictions based on IC50 and ADMET attributes can save the cost of drug evaluation,reduce the occurrence of drug toxicity and side effects,and guide clinically rational drug use.