3D-QSAR,Molecular Docking And Molecular Dynamics Studies Of Targeting DCN1-UBE2M Interaction Inhibitors

Objective:As a post-translational modification of protein,Neddylation is a multi-step cascade enzymatic reaction mediated by NEDD8,which covalently binds to the substrate protein.This catalytic process is completed by the cooperation of NEDD8 activating enzyme,NEDD8 binding enzyme and NEDD8 ligase.Neddylation is abnormally up-regulated in a variety of human tumors and neurodegenerative diseases,so Neddylation is targeted as an attractive method for treating related diseases.Studies have shown that interrupting the DCN1-UBE2M interaction can selectively inhibit Neddylation[1].At present,a series of piperidinyl urea and pyrazolo-pyridone DCN1-UBE2M inhibitors have been discovered by Guy et al.,which have good inhibitory activity.However,the structure-activity relationship of these two types inhibitors has not been reported,and the specific mechanism of action between inhibitors and target proteins is not clear.In this study,molecular simulation studies of these two types inhibitors through computer-aided drug design methods will help clarify the mechanism of interaction between them and DCN1-UBE2M interaction,and provide a theoretical basis for further structural optimization of these two types inhibitors inhibitors.Method:This thesis uses three research methods of computer-aided drug design:molecular docking,molecular dynamics and 3D-QSAR.Molecular docking methods and molecular dynamics methods can analyze the mechanism of action between inhibitors and target proteins.According to the 3D-QSAR method,the CoMFA model and CoMSIA model were established and analyzed to obtain the relationship between the structural characteristics and the activity of the inhibitor.Result:The docking results of piperidinyl urea inhibitors showed that all compounds can bind to the active pocket composed of amino acids such as Ile1083,Ile1086,Phe1089,Pro1097,Phe1109,Ala1111.Thr1113,Gln1114,Phe1117,Phe1164,Met1177,Tyr1181,and Leu 1184,and all compounds are related to the amino acid Gln1114 hydrogen bonds are formed.By comparing the binding modes of compounds 12 and 74,the conformations of the two in the active pockets are quite different,and the binding of compound 74 to the target protein is more stable.Both 12-6BG3 and 74-6BG3 systems have undergone 50ns molecular dynamics simulation.It can be seen from the RMSD trace graph that the 74-6BG3 system tends to stabilize after 25ns,while the 12-6BG3 system has been fluctuating.Comparing the RMSF values of the amino acids of the two systems,it was found that the key amino acids Gln1114,Tyrl 181,Phe1109,Ala1111,Thr1113,and Phe1164 were lower in the 74-6BG3 system than in the 12-6BG3 system.Through hydrogen bond analysis,compound 74 formed significantly more hydrogen bonds with the target protein than compound 12 during the simulation.Combining free energy analysis,Ile1086,Phe1089,Val1102,Ile1105,Ala1106,Gln1114,Phe1164,Met1177 and Tyr1181 were speculated as key amino acids during binding model.The constructed CoMFA model(q2=0.686,r2=0.966,r2pred=0.879)and CoMSIA model(q2=0.682,r2=0.931,r2pred=0.875)both have good prediction ability.Through isopotential analysis,we can understand the relationship between structure and activity.Pyrazolo-pyridone inhibitors can enter the binding site of the target protein,and they may interact with amino acid residues such as Cys1090,Pro1097,Ala1106,Cys1115 and Tyr1181.Based on the common substructure alignment,reliable and predictive CoMFA models(q2=0.533,r2=0.944,r2pred=0.561)and CoMSIA models(q2=0.596,r2=0.976,r2pred=0.687)have been established for such inhibitors.Analyze the equipotential diagram to obtain the relationship between structure and activity.According to the information obtained from the model,30 compounds were designed.Conclusion:Neddylation is an attractive anti-cancer target,and many researchers are working on it.In this study,a series of piperidinyl-urea inhibitors and pyrazolo-pyridone inhibitors were used for computer-aided drug design research.The tools used in the research were molecular docking,molecular dynamics,and 3D-QSAR.Molecular docking can help to understand the mechanism of binding of inhibitors to target proteins,and the important amino acids in the binding process,as well as the effects of hydrogen bonding interactions on the compounds can be obtained.And molecular dynamics is a further verification of the docking results.Two models are established through 3D-QSAR,and their reliability and prediction ability are judged from the statistical parameters of the model.The equipotential diagram of the model can more clearly understand the relationship between inhibitors structure and activity,so as to know which structural characteristics affect the activity of the compounds.On this basis,the pyrazolopyridone inhibitors were optimized,and thirty compounds were tried to be designed.We hope to provide an effective theoretical basis for the design of inhibitors with better activity.This thesis is divided into the follo wing five chapters:The first chapter mainly summarizes the NEDD8,Neddylation process,related enzymes and substrates,and the mechanism of DCN1-UBE2M interaction.Finally,it summarizes the research progress of targeting DCN1-UBE2M inhibitors.Chapter 2:Introduces the calculation methods used in this research,mainly molecular docking,molecular dynamics,and three-dimensional quantitative structure-activity relationship.The development and basic principles of these three calculation methods are mainly explained.Chapter 3:Selected ninety piperidylurea inhibitors from the literature to conduct molecular docking studies to clarify the mode and mechanism of piperidylurea compounds and target protein binding,and then use molecular dynamics simulation to further investigate the more detailed details of piperidylurea inhibitors when binding to the target protein,such as stability and key amino acids,to verify whether the docking results are reliable.Chapter 4:A three-dimensional quantitative structure-activity relationship study of ninety piperidinylurea compounds was constructed,and two reliable and predictive models were constructed,namely the CoMFA model and the CoMSIA model.Analysis based on the equipotential plots of these two models can yield structural features that affect inhibitors activity.This provides some help for further structural modification of piperidylurea inhibitors.Chapter 5:Molecular docking and 3D-QSAR study of fifty-eight pyrazolo-pyridone inhibitors.The molecular docking explains the binding mode of such inhibitors to the target protein.The CoMFA model and CoMSIA model are established by using the common substructure alignment as the alignment method.Analysis of its equipotential diagram can clearly understand the structural features that have an effect on the activity.Based on this,the compounds were optimized,thirty new compounds were designed,and their activities and ADMET were predicted.