O2-2

Prediction of the binding mechanism for DNA
methyltransferase 3A selective inhibitor using molecularsimulation approach
Genki Kudo 1
s2120165@s.tsukuba.ac.jp

Yasuteru Shigeta 2

Ryuhei Harada 2

shigeta@ccs.tsukuba.ac.jp

Takatsugu Hirokawa 3
t-hirokawa@md.tsukuba.ac.jp

ryuhei@ccs.tsukuba.ac.jp

Ryunosuke Yoshino 3
yoshino.r.aa@md.tsukuba.ac.jp1

Physics Department, Graduate School of Pure and Applied Sciences, University of Ts ukuba,
1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan2
Center for Computational Sciences, University of Tsukuba, 1 -1-1 Tennodai, Tsukuba, Ibaraki,305-8577, Japan
3Transborder Medical Research Center, University of Tsukuba, 1 -1-1 Tennodai, Tsukuba, Ibaraki,305-8577, Japan

Keywords: DNA Methyltransferase, Molecular Dynamics, Drug Selectivity
DNA methyltransferase(DNMT) catalyzes the methylation reaction in the DNA cytosine, andseveral isoforms have been reported, such as DNMT1 and DNMT3A. Although the overall
structure of DNMT1 and DNMT3A are different, the active sites of both proteins are similar toeach other [1]. DNA methylation is involved in the inhibition of gene expression, and DNMT
hypermethylation is related to the formation and progression of cancer cells since it causes
inhibition of the tumor suppressor gene [2]. To prevent hypermethylation, many DNMT inhibitors
have been developed. Especially, inhibitors which bind selectivity to specific a DNMT isoform are
attractive because selective drugs are expected to have few side effects [3].
Halby L et al. [4] have reported a selective inhibitor can bind to DNMT3A with about 100 times
more activity than DNMT1. However, the molecular mechanism of selectivity is still unknown
because the complex structure of DNMT3A and any selective inhibitor has not been clarified.
In this study, we predict the complex structure and the residues responsible for binding
selectivity by molecular simulation. Docking simulations were first carried to generate initialstructures of several candidate complexes, and MD simulations were performed to relax thestructures and analyze the stability of complexes. The most stable complex structure wasdetermined by RMSD analyze and the binding free energy using MM/PBSA method. Finally, weanalyzed the energetic contribution of each residue of the protein, interactions, and the structuraldifference with DNMT1. Binding free energy and interaction analysis are suggested that VAL665
and ARG688 of DNMT3A form an interaction with selective inhibitor. Because these residues arereplaced by MET1169 and ASN1192 in DNMT1, compounds that interact with VAL665 andARG688 may selectivity inhibit DNMT3A. In conclusion, we have predicted the complex structureof a DNMT3A–selective inhibitor and the cause of its binding selectivity.
[1] Xie , T.; et al., Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibi tors: amolecular simulation study, Phys Chem Chem Phys, 2019, 21(24), 12931 – 12947.
[2] Saif , I.; et al., Prediction of DNA methylation in the promoter of gene suppressor tumor, Gene,
2018, 651, 166-173.
[3] Yu , J.; et al., DNA methyltransferases: emerging targets for the discovery of inhibitors as potent
anticancer drugs, Drug Discovery Today, 2019, 12, 2323-2331.
[4] Halby, L.; et al., Rational design of bisubstrate-type analogues as inhibitors of DNA
methyltransferases in cancer cells, J Med Chem, 2017, 60(11), 4665 – 4679.