Analysis of the Binding Sites on BAX and the Mechanism of BAX Activators through Extensive Molecular Dynamics Simulations

Abstract

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.

A Step Forward toward Selective Activation/Inhibition of Bak, a Pro-Apoptotic Member of the Bcl-2 Protein Family: Discovery of New Prospective Allosteric Sites Using Molecular Dynamics

“…A NMR structure of the latter is also vailable (2LR1 PDB accession number). These findings suggested that the activation mechanism should be considered as a cooperative process in which multiple sites are involved . These results permit us to speculate that the B1 site can play a similar role in Bak, since the structural domains defining the site are similar in both Bak and Bax.…”

“…However, it has been observed that BAM7 and BTSA1 are able to bind to the deep part of the vMIA site in Bax. 22 These two molecules are known Bax activators, although their role in Bax activation also remains unclear. To fully understand the mechanism behind ligand binding to this site in Bax and Bak, additional docking studies and experimental studies need to be performed to better understand a potential allosteric effect of this site.…”

“…Despite that the mechanism between BH3-only proteins and the antibody is slightly different, there is enough experimental evidence to support a conserved activation mechanism. , Accordingly, further studies focusing on this allosteric site could shed some light into a complete understanding of the Bak activation mechanism and also serve as a guide to design novel allosteric regulators. A recent computational study on the pro-apoptotic Bax has provided information on the identification of prospective allosteric sites that can modulate protein activity . These kinds of studies can be helpful to cope with the challenges associated with finding selective ligands targeting the diverse members of the Bcl-2 family.…”

Molecular Dynamics Simulation-Driven Focused Virtual Screening and Experimental Validation of Inhibitors for MTDH-SND1 Protein–Protein Interaction

“…It is worth noting that there are some well-established computational methods for hotspot searching, such as FTMap , and cosolvent molecular dynamics simulation. − FTMap docks small molecular probes onto the target protein to identify the druggable hotspots on the surface efficiently. The cosolvent molecular dynamics, which shares the similar fundamental principles, could simulate the protein system with the probes, allowing one to identify the potential drug binding pockets in a dynamic manner.…”

Computational Chemistry in Asia

“…Li et al 11 performed extensive MD studies to delineate molecular details of calciuminduced allostery. A cosolvent MD method was employed by Feng et al 12 to detect potential binding sites on the surface of BAX. Chen et al 13 used a randomly accelerated MD algorithm and funnel meta-dynamic simulations to explore the dissociation mechanisms of nonsteroidal GR ligands.…”