K. A. Koo et al. / Bioorg. Med. Chem. Lett. 19 (2009) 2324–2328
2327
Figure 3. (a) Refined docking and (b) surface binding models of HCD160 and compound 18 with Dyrk1A (blue: positive charged region and red: negative charged region).
phobic interaction with Phe 238 and Val 173 residues of Dyrk1A.
Although, the functional groups on both sides of the pyrazolidine-
3,5-diones core scaffold can form a hydrogen bonding interaction
in the ATP binding site, they did not show good inhibition activity
on kinase reaction relative to that of HCD160.
Supplementary data
Supplementary data associated with this article can be found, in
As shown in Figure 3, the docking model of HCD160 and com-
pound 18 with Dyrk1A indicated that the following interactions
are very important in the ATP binding site: the hydrogen bonding
of Asn 244 and Glu 291 side chains, the backbone hydrogen bond-
ing interaction of Met 240 residue, polar (hydrophilic) interaction
of Lys 188, and the hydrophobic interactions of Phe 238 and Val
173. The Dyrk1A inhibition activity and the specificity of com-
pounds tested in this study seems to be dependent on chemical
features such as hydrophobic, hydrophilic, and hydrogen bonding
interactions, as the present compounds were selected by using
References and notes
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TM
PharmoMap for the pharmacophore-based in silico screening.
In the present study, we demonstrated the necessity of the 3-ni-
tro-4-hydroxyphenyl moiety and the p-substituted cyanide group in
the phenyl ring in both sides of the pyrazolidine-3,5-diones core
scaffold, as shown in Figure 3. The presence of those moieties
enhanced the Dyrk1A inhibition activity by blocking autophospho-
rylation of Dyrk1A, as revealed in an in vitro assay. The inhibition as-
say showed relatively good activity for HCD160 and Roscovitine,
which were used as internal controls. Bain et al. reported harmine
as a very potent Dyrk1A inhibitor (IC50 of 0.08
the substrate phosphorylation assay with harmine using our kinase
assay system for comparison. IC50 for harmine was 1 M which was
l
M).8 We performed
l
about 12-times higher than that of the reported IC50 value. This dis-
crepancy could come from a difference in the Dyrk1A protein used in
the assay. We used the 763 amino acid full-length protein while Bain
et al. used the C-terminal truncated 1–499 amino acid protein.
In conclusion, the basic pyrazolidine-3,5-diones core presents a
good scaffold for the development of novel compounds inhibiting
Dyrk1A activity in vitro assay. A more convergent approach and
the design of chemical models for further optimization are needed
to obtain more potent and specific inhibitors. The pyrazolidine-3,5-
diones derivatives could be utilized for the development of novel
therapeutic agents for the treatment of DS related learning and
memory deficits.
Acknowledgments
8. (a) Bain, J.; Plater, L.; Elliott, M.; Shpiro, N.; Hastie, C. J.; McLauchlan, H.;
Klevernic, I.; Arthur, J. S.; Alessi, D. R.; Cohen, P. Biochem. J. 2007, 408, 297; (b)
Bain, J.; McLauchlan, H.; Elliott, M.; Cohen, P. Biochem. J. 2003, 371, 199.
9. For Dyrktide information: (a) Himpel, S.; Tegge, W.; Frank, R.; Leder, S.; Joost, H.
G.; Becker, W. J. Biol. Chem. 2000, 275, 2431; b Kim, N. D.; Yoon, J.; Kim, J. H.;
Lee, J. T.; Chon, Y. S.; Hwang, M. K.; Ha, I.; Song, W. J. Bioorg. Med. Chem. Lett.
2006, 16, 3772. The experimental procedures for assays were described
previously. Briefly, the full-length (763 amino acid) mouse Dyrk1A protein
This work was supported by the Korea Science and Engineering
Foundation (KOSEF) grant funded by the Korea government (R01-
2007-000-11910-0). This work was also supported by the Korea
Research Foundation Grant funded by the Korean Government
(KRF-2007-331-E00031 and KRF-2008-314-E00180).