Computational design of Bax-inhibiting peptides†

Abstract

The proteins of the Bcl-2 family play crucial roles in regulating apoptosis. It is divided into pro-survival and pro-apoptotic proteins that determine cellular fate. In particular, Bax is a crucial executor of apoptosis as its activation initiates the apoptotic phenotype. Hence, targeting this protein represents an attractive therapeutic approach, which can aid in regulating apoptotic signalling and potentially contribute to the development of novel therapies against cancer and neurodegenerative diseases. Here, we introduce a digital paradigm, which relies on rational design and computer simulations to develop and validate peptide-based agents that bind to Bax, thereby inhibiting its apoptotic properties. The peptides are rationally designed and optimized to bind to Bax starting from the crystal structures of affimers in a complex with Bcl-2 proteins. Next, molecular dynamics (MD) simulations are employed to probe the stability of the Bax–peptide complexes and to estimate the binding free energies. The results show that the designed peptides bind with high affinity to Bax. Two of the designed peptides bind in the canonical hydrophobic groove (BH1 domain) of Bax and one peptide binds to the outside of the BH3 domain (α₂-helix). Notably, the peptides restrict the flexibility of the α₁–α₂ loop, modulating the trigger bottom site associated with toxicity. All in all, the results highlight the potential of these peptides as valuable tools for further exploration in modulating apoptotic pathways and set the structural foundation for a machine learning powered engine for peptide design.