Insight Into The Selective Binding Mechanism Of DNMT Inhibitors And Discovery Of DNMT1 Inhibitors

DNA methylation is a major epigenetic modification that regulates gene expression in the genome of higher eukaryotes.Hypermethylation of promoter CpG islands can turn off the expression of tumor suppressor genes（TSGs）,leading to the occurrence of many types of tumors.Because the DNA methylation process is reversible,removing aberrant methylation can restore the TSG expression and then revert cancer cells to their normal states,which provides possibility to develop new strategies for tumor therapy.Therefore,DNA methylethyltransferases（DNMTs）have been regarded as promising drug targets.Although a number of non-nucleoside DNMT inhibitors（DNMTi）have been reported,most of them are not quite promising because of weak inhibition activity or low specificity.Until now,none of the non-nucleoside DNMT inhibitors has been approved by the US Food and Drug Administration（FDA）.Discovery of novel non-nucleoside DNMTi with specific selectivity and high potency is quite urgent.In this thesis,multiple molecular simulation methods were employed to explore the structural differences in the active sites of DNMT1 and DNMT3A related to selectivity and activity of inhibitors.Then,based on the information provided by molecular modeling,structure-based drug design was performed to discover effective and selective inhibitors towards DNMT1.In the first part of this thesis,the binding selectivity of three representative non-nucleoside DNMT inhibitors,including SFG,DC₀5 and GSKex1,towards DNMT1 and DNMT3A was studied by molecular dynamics（MD）simulations,Molecular Mechanics/Generalized Born Surface Area（MM/GBSA）free energy calculations and other methods.The results of the MM/GBSA free energy calculation combined with the structure analysis are in good agreement with the experimental data.According to the results provided by the MM/GBSA free energy decomposition,the important residues for the binding of small molecules were determined,suggesting that the van der Waals interactions between non-conserved residues and small molecules are the most important contributor to inhibitor selectivity.Val1580/Trp893,Asn1578/Arg891 and Met1169/Val665 have a significant effect on the selectivity of DNMT inhibitors,and they have a great impact on theπ-πstacking and hydrogen bonding interactions.The study provide important structural information for the design of potential selective DNMT inhibitors,and lay the theoretical foundation for the subsequent design of DNMT1inhibitors.In the second part of this thesis,docking-based virtual screening was used to identify DNMT1 inhibitors.More than 1.4 million small molecules in the Chemdiv compound library were screened by two docking methods,Glide and Autodock vina.In accordance with the research results in the first part of this thesis,the screened compounds were evaluated by the scoring functions.Then,the compounds with reasonable binding patterns and high docking scores were selected for subsequent bioassays.The results of in vitro enzyme activity experiments show that i38 series compounds have good activity against DNMT1.The IC₅₀（DNMT1）of the best compound is 67μM,which is expected to be a potential lead compound for the treatment of DNMT1-related cancers.At the same time,the discovery of i38 series also lays the foundation for the design and modification of DNMT1 selective inhibitors.