Homology modeling of protein kinase ATR complexed with its ...

KO-06
Homology modeling of protein kinase ATR complexed with
its inhibitor
Teruyo YONEDA, * Hiroaki KODERA, Minoru TAMIYA, Masaji ISHIGURO
Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences
1. Introduction
ATM (ataxia-telangiectasia mutated) and ATR (ATM and Rad3-related) are protein kinases that
play a crucial role in cellular DNA damage response. They are activated by DNA damage and
function in cell-cycle checkpoint signaling [1]. Though a specific ATR inhibitor has not yet been
discovered, recently it is found that schizandrin inhibits ATR kinase activity in vitro, and disrupts
G2/M checkpoint repair following UV irradiation [2]. Schizandrin is a dibenzocyclooctadiene
derivative from Fructus Schisandrae, gomishi in Japanese, a traditional Chinese medicine. As the
disruption of DNA damage repair can be favorable for therapeutic treatment of cancer, ATR
inhibitors may present radio/chemo-sensitizing agents for cancer therapy. In this paper, we report
the modeling of the tertiary structure of ATR kinase domain complexed with schizandrin and its
diastereomer. Analysis of their interaction may provide the knowledge to design novel derivatives of
ATR inhibitors.
2. Methods
ATR is a member of phosphoinositide 3-kinase related kinases (PIKKs) and has a catalytic
domain homologous to that of PI 3-kinases. Thus we constructed a structural model of a human
ATR kinase domain based on the crystal structure of the catalytic domain of human PI3Kγ (PDB
code: 2CHX) by homology modeling. As the structure of an activation loop of the template was not
determined, we used an activation loop of mouse cAMP-dependent protein kinase complexed with
ATP and Mn 2+ ions (PDB code: 1ATP). Then schizandrin (Fig.1) was bound to the ATP-binding site
of the obtained homology model by auto-docking, followed by molecular dynamics (MD)
calculation with water solvent molecules. The modeling software MOE (CCG Inc.) was used for
homology modeling, docking, and MD calculation.
tyoneda@nupals.ac.jp
O
H 3CO
H 3CO
H 3CO
O
OCH 3
H
H
(M)-γ−schizandrin
O
H 3CO
H 3CO
H 3CO
O
OCH 3
H
H
(P)-(−)-gomisin N
Fig.1. Schizandrin and its diastereomer

2. Results and Discussion
The auto-docking calculation gave several tens of binding poses, in a part of those the
configuration of the ligand changed from the initial stereoisomer, (M)-γ−schizandrin, to its
diastereomer, (P)-(−)-gomisin N. Through the inspection of binding models we finally obtained two
complex models, shown in Fig.2. The hydrogen bonds formed between important residues of the
ATP-binding site and the individual ligands were indicated by dushed line for both models in Fig.2.
In ATR-(M)-γ−schizandrin complex model (Fig.2a), Val2380 and Lys2327 formed hydrogen bonds
with the ligand, and in ATR-(P)-(−)-gomisin N complex model (Fig.2b), Val2380 and Trp2379
formed. These results suggest that the methylenedioxy ring of schizandrin may play a similar role to
an adenine ring of ATP in the ATP-binding site of ATR.
We are now synthesizing schizandrin derivatives to confirm the binding mode by binding
experiments with ATR.
(a)
Val2380
Trp2379
Lys2327
Acknowledgements
We wish to thank Drs T. Konishi and H. Nishida of Niigata Univ. of Pharm. Appl. Life Sci. for the
biological information about schizandrin and its related compounds.
References
[1] S. Matsuoka et al., Science 2007, 316, 1160-1166.
[2] H. Nishida et al., Nucleic Acids Res. 2009, 1-12.
(b)
Val2380
Trp2379
Fig.2. Interaction of ligands with residues of ATP-binding site. (a) ATR-
(M)-γ−schizandrin complex. (b) ATR-(P)-(−)-gomisin N complex.