Structure of human protein kinase CK2α2 with a potent indazole-derivative inhibitor

Abstract

Casein kinase 2 (CK2) is a serine/threonine kinase that functions as a heterotetramer composed of two catalytic subunits (CK2alpha1 or CK2alpha2) and two regulatory subunits (CK2beta). The two isozymes CK2alpha1 and CK2alpha2 play distinguishable roles in healthy subjects and in patients with diseases such as cancer, respectively. In order to develop novel CK2alpha1-selective inhibitors, the crystal structure of human CK2alpha2 (hCK2alpha2) complexed with a potent CK2alpha inhibitor which binds to the active site of hCK2alpha2 was determined and compared with that of human CK2alpha1. While the two isozymes exhibited a high similarity with regard to the active site, the largest structural difference between the isoforms occurred in the beta4-beta5 loop responsible for the CK2alpha-CK2beta interface. The top of the N-terminal segment interacted with the beta4-beta5 loop via a hydrogen bond in hCK2alpha2 but not in hCK2alpha1. Thus, the CK2alpha-CK2beta interface is a likely target candidate for the production of selective CK2alpha1 inhibitors.

Structure of the Human Protein Kinase CK2 Catalytic Subunit CK2α′ and Interaction Thermodynamics with the Regulatory Subunit CK2β

“…Extensive crystallization screens to obtain hsCK2α′ Cys336Ser crystals were performed. Under various conditions, hsCK2α′ Cys336Ser forms very tiny and fragile crystalline needles that are similar in appearance to the hsCK2α′ ΔC /3E3B crystals pictured by Nakaniwa et al 22 We were (a) Lineweaver-Burk plot of a Michaelis-Menten kinetic test series with hsCK2α′ Cys336Ser (red) and hsCK2α 1-335 (blue), using variable initial concentrations of ATP. Each point represents the average of three independent experiments.…”

“…Therefore, we wanted to supplement the hsCK2α′ Cys336Ser structure of this work with the aforementioned hsCK2α′ ΔC /3E3B structure, 22 in particular since it belongs to a different crystal form. An inspection of this structure, however, strongly suggested further refinement prior to structural comparisons and discussions.…”

“…20,21 A first attempt to clarify differences between hsCK2α and hsCK2α′ at a structural level was published by Nakaniwa et al, who determined a crystal structure of an hsCK2α′ construct [Protein Data Bank (PDB) code 3E3B] that was C-terminally truncated and thus missed one of the candidate regions for differences between the two paralog isoforms. 22 Here we refer to this structure as "hsCK2α′ ΔC /3E3B" (the C-terminal truncation mutant of human CK2α′ underlying PDB entry 3E3B), compare it with our own high-quality structure of an hsCK2α′ construct, and present subtle structural deviations between hsCK2α′ and hsCK2α that may account for differences between the two isoforms' affinity for CK2β.…”

“…1a), we wanted to produce the full-length protein in order to preserve the unique sequence zone and potential distinction region from hsCK2α. 22 In fact, we were able to obtain a well-soluble full-length construct (hereon referred to as hsCK2α′ Cys336Ser , the point mutant Cys336Ser of human CK2α′) by mutation of Cys336 to serine. We had noticed the critical character of this cysteine residue during preceding studies with a chimeric construct comprising residues 1-325 of hsCK2α and residues 327-350 of hsCK2α′; preparations of this construct had shown the slow but significant tendency to dimerize covalently as a result of intermolecular disulfide bridges formed by Cys336 (unpublished results).…”

How druggable is protein kinase CK2?

“…168 Recently, the X-ray diffraction crystallographic spectra of the most promising compound of the series (CC04820, IC 50 value of 0.017 mM) in complex with CK2 169 has been solved. The binding mode of the inhibitor resembles to the position of IQA and in particular the acetic acid moieties of the two molecules have a comparable location in the enzyme pocket.…”