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

• Published in: Molecular informatics 2019-03, Vol.38 (3), p.e1800089-n/a
• Main Authors: Tang, Shan, Zhang, Na, Zhou, Yue, Cortopassi, Wilian A., Jacobson, Matthew P., Zhao, Li‐jiao, Zhong, Ru‐gang
• Format: Article
• Language: English
• Subjects: Affinity; Amino Acid Substitution; Amino acids; Antagonists; anti-canceractivity; Antineoplastic Agents - chemistry; Antineoplastic Agents - pharmacology; Apoptosis; Apoptosis - drug effects; ATP; Binding; binding affinity; Binding Sites; Business competition; Cancer; Casein kinase II; Casein Kinase II - antagonists & inhibitors; Casein Kinase II - chemistry; Casein Kinase II - genetics; Casein Kinase II - metabolism; Computer applications; Computer simulation; cyclic peptides; Drug Discovery; Dynamic structural analysis; Hep G2 Cells; Humans; Inhibitors; Kinases; Molecular Docking Simulation; Molecular dynamics; Optimization; Peptides; Peptides, Cyclic - chemistry; Peptides, Cyclic - pharmacology; Personal computers; Protein Binding; Protein kinase C; Protein kinase CK2; Protein Kinase Inhibitors - chemistry; Protein Kinase Inhibitors - pharmacology; Proteins; Quantitative Structure-Activity Relationship; Selectivity; Target recognition
• ISSN: 1868-1743; 1868-1751
• DOI: 10.1002/minf.201800089

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 CK2α/CK2β interface as CK2 holoenzyme antagonists. Here we improved the binding affinity to CK2α and cell‐based anti‐cancer activity of a CK2β‐derived cyclic peptide (Pc) by combining structure‐based computational design with experimental evaluation. By analyzing molecular dynamics simulations of Pc bound to CK2α, a series of Pc‐derived peptides was rationally designed and synthesized to evaluate their binding affinity to CK2α, 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 CK2α 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 (∼5×) to CK2α. The discovery of the I192F and H193W peptides provides new insights for further optimization of CK2 antagonist candidates as anti‐cancer leads.