Protein kinase B (PKB) plays a key role in the phosphoinositide 3-kinase pathway,
one of the most frequently activated proliferation pathways in cancer. A key stage in
this pathway is PKB’s translocation to the plasma membrane, which is driven by
direct interaction of PKB’s pleckstrin homology (PH) domain with the inositol
phosphate head-groups of phosphoinositide lipids PtdIns(3,4,5)P3 and PtdIns(3,4)P2.
In this thesis a computational approach has been applied to study the interaction
between PKB’s PH domain and the inositol phosphate head-groups of
phosphoinositide lipids. Herein the first full set of parameters for these inositol
phosphates has been generated using a clearly defined algorithmic approach. The
parameters have been applied in a total of 6 μs of molecular dynamics (MD)
simulations to investigate the interaction between inositol phosphates and the PKB
PH domain. The simulations successfully mirror, and additionally rationalise, PKB’s
experimental interactions and behaviour. As well as investigating the native system, a
PKB mutant that has been reported in multiple human cancers has also been explored.
This PKB mutant constitutively targets the plasma membrane due to its broadened
phosphoinositide selectivity. The atomic-level view available from MD simulations
has helped elucidate the molecular mechanism behind this.
Information obtained about the PKB PH domain’s binding interface has been used to
design inositol phosphate derivatives to inhibit PKB activation. MD simulations have
allowed a number of inositol phosphate derivatives to be rapidly screened for their
inhibitory behaviour. The predicted behaviour of a select number of these derivatives
has been further assessed using biochemical techniques. Gratifyingly, the
computational and biochemical results are shown to be in good agreement.