Dynamics insights into CDK4/6-CyclinD1 complex stability modulated by abemaciclib

The CDK4/6-CyclinD1 complex, a fundamental component of the cell cycle regulatory mechanism, is associated with numerous cancers. The synergistic action of P21 and P27 is essential for regulating the G1/S transition in the cell cycle. Current HDX-MS and other experimental studies enhance the understanding of P21 and P27 binding to the CDK4-CyclinD1 complex in response to abemaciclib treatment. However, the existing knowledge of the abemaciclib's effect on the stability of the CDK4/6-CyclinD1-P21/P27 complex is still limited. Here, we utilize molecular dynamics simulations to quantitatively assess specific regions and delineate the roles of individual subsystems or residues through energy decomposition methods. Our results, derived from residue decomposition via molecular dynamics simulations and RIN analysis, reveal that P21 binding to the CDK4 complex involves a broader set of residues and exhibits a higher binding affinity compared to CDK6. Moreover, in the CDK4-CyclinD1-P21 complex, abemaciclib tends to disrupt the C-lobe region of CDK4. To validate this hypothesis, a sequence mutant of the C-terminus of CDK4 was generated, showing that the C-terminus of CDK4 selectively modulates the abemaciclib-mediated decrease in the P21 binding affinity. These findings significantly enhance our understanding of the broader non-catalytic mechanisms underlying second-generation CDK4/6 inhibitors. It is expected that second-generation inhibitors will further destabilize the CDK6-CyclinD1-P21 complex and the P27-containing complex, thereby improving the efficacy of CDK4/6 inhibitors as cancer therapies.