Theoretical study on the selective binding of BH3-only protein BAD to anti-apoptotic protein BCL-xL instead of MCL-1

In this study, molecular dynamics simulations were used to systematically explore the reason why BH3-only protein BAD binds to anti-apoptotic protein BCL-xL but not to MCL-1 to give more theoretical hints for the design of BAD mimetic inhibitors for the dual-targeting of BCL-xL and MCL-1. Starting with the difference in residue-based binding energy contributions, a series of analyses were conducted to identify the hotspot residues in MCL-1 that significantly affect the interaction with BAD. Among them, the insertion of the T residue in the loop between α4 and α5 domains of MCL-1 is considered to be the main cause of BAD selective binding. The inserted T residue reduces the stability of the loop and weakens the hydrogen bond interactions that originally bound E19 of BAD in BCL-xL/BAD, and the freed E19 severely interferes with the salt bridge between D16 and Arg53 by electrostatic repulsion. This salt-bridge is believed to be critical for maintaining the binding between BCL-xL and BAD. By clarifying the reasons for differential binding, we can more specifically optimize the BAD sequence to target both BCL-xL and MCL-1.