Molecular mechanisms underlying HRK interaction with BCL-XL and BCL-2 reveal specificity determinants for BH3 mimetics.

BH3 mimetics targeting the BCL-2 family hold broad promise for cancer therapy. High similarity between the anti-apoptotic proteins BCL-XL and BCL-2 challenges the engineering of selective inhibitors. The BH3-only protein HRK is a natural selective inhibitor of BCL-XL and to a less extent of BCL-2. The detailed interaction mechanism remains elusive. Our structural and mutational analyses show that the discrepant conformational changes and non-conserved residues in the α2-α3 region are crucial for the preferential binding between BCL-XL and HRK. BCL-XL tolerates hydrophilic Thr33 or hydrophobic substitutions at the h1 position of HRK, whereas BCL-2 favors hydrophobic interactions, resulting in a weaker affinity for HRK. In addition, we design HRK-derived stapled peptides with improved helicity and activity against BCL-XL and BCL-2, and further elucidate the structural mechanism. Our findings reveal the binding specificity of HRK interactions with BCL-XL and BCL-2, and provide advanced insights into the development of BH3 mimetics.