2-Aminomethylthieno[3,2-d]pyrimidin-4(3H)-ones bearing 3-methylpyrazole hinge binding moiety: Highly potent, selective, and time-dependent inhibitors of Cdc7 kinase

Osamu Kurasawa; Misaki Homma; Yuya Oguro; Tohru Miyazaki; Kouji Mori; Noriko Uchiyama; Kenichi Iwai; Akihiro Ohashi; Hideto Hara; Sei Yoshida; Nobuo Cho

doi:10.1016/j.bmc.2017.04.044

2-Aminomethylthieno[3,2-d]pyrimidin-4(3H)-ones bearing 3-methylpyrazole hinge binding moiety: Highly potent, selective, and time-dependent inhibitors of Cdc7 kinase

Bioorg Med Chem. 2017 Jul 15;25(14):3658-3670. doi: 10.1016/j.bmc.2017.04.044. Epub 2017 May 2.

Authors

Affiliations

¹ Pharmaceutical Research Division, Takeda Pharmaceutical Company, Ltd., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. Electronic address: [email protected].
² Pharmaceutical Research Division, Takeda Pharmaceutical Company, Ltd., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.

PMID: 28533114
DOI: 10.1016/j.bmc.2017.04.044

Abstract

In order to increase the success rate for developing new Cdc7 inhibitors for cancer therapy, we explored a new chemotype which can comply with the previously-constructed pharmacophore model. Substitution of a pyridine ring of a serendipitously-identified Cdc7 inhibitor 2b with a 3-methylpyrazole resulted in a 4-fold increase in potency and acceptable kinase selectivity, leading to the identification of thieno[3,2-d]pyrimidin-4(3H)-one as an alternative scaffold. Structure-activity relationship (SAR) study revealed that incorporation of a substituted aminomethyl group into the 2-position improved kinase selectivity. Indeed, a pyrrolidinylmethyl derivative 10c was a potent Cdc7 inhibitor (IC₅₀=0.70nM) with high selectivity (Cdk2/Cdc7≥14,000, ROCK1/Cdc7=200). It should be noted that 10c exhibited significant time-dependent Cdc7 inhibition with slow dissociation kinetics, cellular pharmacodynamic (PD) effects, and COLO205 growth inhibition. Additionally, molecular basis of high kinase selectivity of 10c is discussed by using the protein structures of Cdc7 and Cdk2.

Keywords: Cell division cycle 7 (Cdc7); Thieno[3,2-d]pyrimidin-4(3H)-one; Time-dependent Cdc7 inhibition.

MeSH terms

Binding Sites
Cell Cycle Proteins / antagonists & inhibitors*
Cell Cycle Proteins / genetics
Cell Cycle Proteins / metabolism
Cyclin-Dependent Kinase 2 / antagonists & inhibitors
Cyclin-Dependent Kinase 2 / metabolism
Humans
Inhibitory Concentration 50
Kinetics
Molecular Docking Simulation
Protein Binding
Protein Kinase Inhibitors / chemical synthesis
Protein Kinase Inhibitors / chemistry*
Protein Kinase Inhibitors / pharmacokinetics
Protein Serine-Threonine Kinases / antagonists & inhibitors*
Protein Serine-Threonine Kinases / genetics
Protein Serine-Threonine Kinases / metabolism
Protein Structure, Tertiary
Pyrazoles / chemistry*
Pyrimidinones / chemical synthesis
Pyrimidinones / chemistry*
Pyrimidinones / pharmacokinetics
Recombinant Proteins / biosynthesis
Recombinant Proteins / chemistry
Recombinant Proteins / genetics
Structure-Activity Relationship
Thiophenes / chemical synthesis*
Thiophenes / chemistry
Thiophenes / pharmacokinetics
rho-Associated Kinases / antagonists & inhibitors
rho-Associated Kinases / genetics
rho-Associated Kinases / metabolism

Substances

6-(3-methyl-1H-pyrazol-4-yl)-2-(pyrrolidin-1-ylmethyl)thieno(3,2-d)pyrimidin-4(3H)-one
Cell Cycle Proteins
Protein Kinase Inhibitors
Pyrazoles
Pyrimidinones
Recombinant Proteins
Thiophenes
CDC7 protein, human
Protein Serine-Threonine Kinases
ROCK1 protein, human
rho-Associated Kinases
Cyclin-Dependent Kinase 2
3-methylpyrazole