The BAX protein is a pro-apoptotic
member of the Bcl-2 family,
which triggers apoptosis by causing permeabilization of the mitochondrial
outer membrane. However, the activation mechanism of BAX is far from
being understood. Although a few small-molecule BAX activators have
been reported in the literature, their crystal structures in complex
with BAX have not been resolved. So far, their binding modes were
modeled at most by simple molecular docking efforts. Lack of an in-depth
understanding of the activation mechanism of BAX hinders the development
of more effective BAX activators. In this work, we employed cosolvent
molecular dynamics simulation to detect the potential binding sites
on the surface of BAX and performed a long-time molecular dynamics
simulation (50 μs in total) to derive the possible binding modes
of three BAX activators (i.e., BAM7, BTC-8, and BTSA1) reported in
the literature. Our results indicate that the trigger, S184, and vMIA
sites are the three major binding sites on the full-length BAX structure.
Moreover, the canonical hydrophobic groove is clearly detected on
the α9-truncated BAX structure, which is consistent with the
outcomes of relevant experimental studies. Interestingly, it is observed
that solvent probes bind to the trigger bottom pocket more stably
than the PPI trigger site. Each activator was subjected to unbiased
molecular dynamics simulations started at the three major binding
sites in five parallel jobs. Our MD results indicate that all three
activators tend to stay at the trigger site with favorable MM-GB/SA
binding energies. BAM7 and BTSA1 can enter the trigger bottom pocket
and thereby enhance the movement of the α1−α2 loop,
which may be a key factor at the early stage of BAX activation. Our
molecular modeling results may provide useful guidance for designing
smart biological experiments to further explore BAX activation and
directing structure-based efforts toward discovering more effective
BAX activators.