Molecular modeling studies of the Akt PH domain and its interaction with phosphoinositides

The serine-threonine protein kinase Akt is a direct downstream target of ph osphatidylinositol 3-kinase (PI3-K). The PI3-K-generated phospholipids regu late Akt activity via directly binding to the Akt PH domain. The binding of PI3-K-generated phospholipids is critical to the relocalization of Akt to the plasma membrane, which plays an important role in the process of Akt ac tivation. Activation of the PI3-K/Akt signaling pathway promotes cell survi val. To elucidate the structural basis of the interaction of PI3-K-generate d phospholipids with the Akt PH domain with the objective of carrying out s tructure-based drug design, we modeled the three-dimensional structure of t he Akt PH domain. Comparative modeling-based methods were employed, and the modeled Akt structure was used in turn to construct structural models of A kt in complex with selected PIS-K-generated phospholipids using the computa tional docking approach. The model of the Akt PH domain consists of seven b eta -strands forming two antiparallel beta -sheets capped by a C-terminal a lpha -helix. The beta1-beta2, beta3-beta4, and beta6-beta7 loops form a pos itively charged pocket that can accommodate the PI3-K-generated phospholipi ds in a complementary fashion through specific hydrogen-bonding interaction s. The residues Lys14, Arg25, Tyr38, Arg48, and Arg86 form the bottom of th e binding pocket and specifically interact with the 3- and 4-phophate group s of the phospholipids, while residues Thr21 and Arg23 are situated at the wall of the binding pocket and bind to the l-phosphate group. The predicted binding mode is consistent with known site-directed mutagenesis data, whic h reveal that mutation of these crucial residues leads to the loss of Akt a ctivity. Moreover, our model can be used to predict the binding affinity of PI3-K-generated phospholipids and rationalize the specificity of the Akt P H domain for PI(3,4)P2, as opposed to other phospholipids such as PI(3)P an d PI(3,4,5)P3. Taken together, our modeling studies provide an improved und erstanding of the molecular interactions present between the Akt PH domain and the PIS-K-generated phospholipids, thereby providing a solid structural basis for the design of novel, high-affinity ligands useful in modulating the activity of Akt.