Underlying mechanisms of cyclic peptide inhibitors interrupting the interaction of CK2α/CK2β: comparative molecular dynamics simulation studies

Protein-protein interactions (PPIs) are fundamental to all biological processes. Recently, the CK2 beta-derived cyclic peptide Pc has been demonstrated to efficiently antagonize the CK2 alpha/CK2 beta interaction and strongly affect the phosphorylation of CK2 beta-dependent CK2 substrate specificity. The binding affinity of Pc to CK2 alpha is destroyed to different extents by two single-point mutations of Tyr188 to Ala (Upsilon 188A) and Phe190 to Ala (F190A), which exert negative effects on the inhibitory activity (IC50) of Pc against the CK2 alpha/CK2 beta interaction from 3.0 mu M to 54.0 mu M and >> 100 mu M, respectively. However, the structural influences of Upsilon 188A and F190A mutations on the CK2 alpha-Pc complex remain unclear. In this study, comparative molecular dynamics (MD) simulations, principal component analysis (PCA), domain cross-correlation map (DCCM) analysis and energy calculations were performed on wild type (WT), Upsilon 188A mutant, and F190A mutant systems. The results revealed that ordered communications between hydrophobic and polar interactions were essential for CK2 alpha-Pc binding in the WT system. In addition to the loss of the hydrogen bond between Gln36 of CK2 alpha and Gly189 of Pc in the two mutants, the improper recognition mechanisms occurred through different pathways. These pathways included the weakened hydrophobic interactions in the Upsilon 188A mutant as well as decreased polar and hydrophobic interactions in the F190A mutant. The energy analysis results qualitatively elucidated the instability of the two mutants and energetic contributions of the key residues. This study not only revealed the structural mechanisms for the decreased binding affinity of Upsilon 188A and F190A mutant CK2 alpha-Pc complexes, but also provided valuable clues for the rational design of CK2 alpha/CK2 beta subunit interaction inhibitors with high affinity and specificity.