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Protein kinase CK2 is a multi-subunit complex whose dynamic assembly appears as a crucial point of regulation. The ability to interfere with specific protein–protein interactions has already provided powerful means of influencing the functions of selected proteins within the cell. CK2β-derived cyclopeptides that target a well-defined hydrophobic pocket on CK2α have been previously characterized as potent inhibitors of CK2 subunit assembly [9]. As a first step toward the rational design of low molecular weight CK2 antagonists, we have in the present study screened a collection of podophyllotoxine indolo-analogues to identify chemical inhibitors of the CK2 subunit interaction. We report the identification of a podophyllotoxine indolo-analogue as a chemical ligand that binds to the CK2α/CK2β interface inducing selective disruption of the CK2α/CK2β assembly and concomitant inhibition of CK2α activity.