Diacritic Binding of an Indenoindole Inhibitor by CK2α Paralogs Explored by a Reliable Path to Atomic Resolution CK2α′ Structures

Abstract

CK2α and CK2α′ are the two isoforms of the catalytic subunit of human protein kinase CK2, an important target for cancer therapy. They have similar, albeit not identical functional and structural properties, and were occasionally reported to be inhibited with distinct efficacies by certain ATP-competitive ligands. Here, we present THN27, an indeno[1,2-b]indole derivative, as a further inhibitor with basal isoform selectivity. The selectivity disappears when measured using CK2α/CK2α′ complexes with CK2β, the regulatory CK2 subunit. Co-crystal structures of THN27 with CK2α and CK2α′ reveal that subtle differences in the conformational variability of the interdomain hinge region are correlated with the observed effect. In the case of CK2α′, a crystallographically problematic protein so far, this comparative structural analysis required the development of an experimental strategy that finally enables atomic resolution structure determinations with ab initio phasing of potentially any ATP-competitive CK2 inhibitor and possibly many non-ATP-competitive ligands as well bound to CK2α′.

Structural and Mechanistic Basis of the Inhibitory Potency of Selected 2-Aminothiazole Compounds on Protein Kinase CK2

“…Allosteric CK2α binding site of 2-aminothiazole derivatives reported by Bestgen et al and its principle accessibility within the CK2α′ crystal packing used for this study. (a) In silico complex of CK2α, CX-4945, and 27 modeled by Bestgen et al (b) View along a solvent channel within the crystal packing of the CK2α′ Cys336Ser /MB002 complex (PDB code 6HMQ) surrounded by symmetry equivalents; in addition, 27 is drawn after the overlay of the in silico complex in panel a on CK2α′ Cys336Ser . The pictures were generated with Pymol …”

Synthesis and SAR of Tetracyclic Inhibitors of Protein Kinase CK2 Derived from Furocarbazole W16

“…In addition to analyzing the influence of the test compounds on the CK2α/CK2β interaction, the inhibition of the enzymatic activity of the holoenzyme (CK2α 2 β 2 ), the CK2α subunit, and the mutated CK2α’ C336S subunit was investigated in a capillary electrophoresis (CE) assay. In this assay, the decapeptide RRRDDDSDDD, a known class I substrate suitable for assaying the kinase activity of both the CK2 holoenzyme and the catalytically active CK2 subunits, was reacted with ATP in the presence of enzyme, which transfers a phosphate group to Ser7 of the decapeptide. Due to the additional negative charge of the phosphate group, the decapeptide and the phosphorylated decapeptide can be separated by CE.…”

Mechanistic insights of key host proteins and potential repurposed inhibitors regulating SARS‐CoV‐2 pathway

“…It is crucial when the host has antibodies developed for SARS-CoV-2 by vaccination or recovery from COVID-19 infection and is still susceptible to new variants. 11 The Caesin Kinase 2 (CK2), 12,13 Histone deactylease (HDAC2), 14,15 and eIF4E2 host proteins are essential for the normal functioning of cells, involved in cell cycle checkpoints, metabolic pathways, epigenetic regulators, mRNA translation pathways. These proteins get perturbed in the cancerous cells.…”