Structure-based Discovery of Novel CK2α-Binding Cyclic Peptides with Anti-cancer Activity

Protein kinase CK2 is considered as an emerging target in cancer therapy, and recent efforts have been made to develop its ATP-competitive inhibitors, but achieving selectivity with respect to related kinases remains challenging because of the highly conserved ATP-binding pocket of kinases. Non-ATP competitive inhibitors might solve this challenge; one such strategy is to identify compounds that target the CK2 alpha/CK2 beta interface as CK2 holoenzyme antagonists. Here we improved the binding affinity to CK2 alpha and cell-based anti-cancer activity of a CK2 beta-derived cyclic peptide (Pc) by combining structure-based computational design with experimental evaluation. By analyzing molecular dynamics simulations of Pc bound to CK2 alpha, a series of Pc-derived peptides was rationally designed and synthesized to evaluate their binding affinity to CK2 alpha, as well as anti-proliferative and pro-apoptotic effects against HepG2 cancer cell line. One amino acid substitutions on Pc, I192F, exhibited over 10-fold improvement in the predicted binding affinity to CK2 alpha when compared to Pc, and a cell-permeable version, I192F-Tat, also demonstrated more potent anti-proliferative and pro-apoptotic effects against HepG2 compared to Pc. A second modification of Pc, H193W, also led to more potent cell-based activity, despite having weaker binding affinity (similar to 5x) to CK2 alpha. The discovery of the I192F and H193W peptides provides new insights for further optimization of CK2 antagonist candidates as anti-cancer leads.