Selective targeting of Aurora kinase B over A: Uncovering the structural basis for inhibitor specificity through molecular dynamics simulations

As promising therapeutic targets for various types of cancers, Aurora kinases A and B share high sequence and structural similarity, posing a challenge for designing subtype-selective small-molecule inhibitors. Since Aurora kinase A functions as both an oncogene and a haploinsufficient tumor suppressor, selectively inhibiting Aurora kinase B with highly specific inhibitors offers a less toxic anti-cancer strategy. However, the molecular mechanism governing ligand selectivity for Aurora kinase B over A remains unclear. In this study, we used Barasertib, an experimentally validated ligand with 1000-fold selectivity for Aurora kinase B over A, as a template molecule to investigate the selectivity mechanism through molecular dynamics simulations and binding free energy analyses. Our studied showed that in the ATP-binding pocket, the hinge residue Arg159 (-2.21 kcal/mol), exclusive to Aurora kinase B, significantly contributed to Barasertib binding, whereas no such binding occurred with the corresponding residue Leu215 (-0.10 kcal/mol) in Aurora kinase A. In the hydrophobic back pocket, the sum of binding free energies for key residues Lys106, Glu125, and Asp218 in Aurora kinase B (-4.02 kcal/ mol) was substantially lower than that (7.89 kcal/mol) for the corresponding residues Lys162, Glu181, and Asp274 in Aurora kinase A. This finding suggests that binding interactions at the hydrophobic back pocket play a crucial role in Barasertib's selectivity for Aurora kinase B over A. Interestingly, in contrast to the complexes without partner proteins, the binding of partner proteins in both Aurora kinase A and B models induced the aC helix and the beta sheets in the N-lobe to move inward towards the ATP-binding pocket, resulting in a smaller hydrophobic back pocket and unfavorable Barasertib binding. In summary, our results demonstrate how differential ligand behavior arises from a complex interplay of subtle but relevant structural differences upon binding to distinct kinase subtypes. The insights into the structural determinants of subtype selectivity will facilitate the development of highly selective and potent Aurora kinase B inhibitors as drug candidates for cancer therapy.