Structural analysis of apoptotic MCL1-HRK complex

Myeloid cell leukemia 1 (MCL1) is an anti-apoptotic protein belonging to the BCL-2 family, which inhibits mitochondrial apoptosis by counteracting pro-apoptotic proteins. A significant number of malignant cells rely on MCL1 for their survival, and the suppression of MCL1 using BH3 mimetics is regarded as a promising anticancer approach. In this study, biochemical binding assays demonstrated that a BH3 peptide from Harakiri (HRK), a pro-apoptotic BH3-only sensitizer, exhibited a moderate affinity for MCL1 with an EC₅₀ of 42.7 nM. The structure of MCL1 complexed with the HRK BH3 peptide was subsequently resolved at 1.4 Å resolution. Structural analysis indicates that the α-helical HRK BH3 occupies the canonical hydrophobic groove on the MCL1 surface. Three leucine residues situated in the core BH3 region and two hydrophilic threonine residues on either side insert into the small hydrophobic pockets of the MCL1 groove. The charged residue K38 and the highly conserved D42 interact with the conserved D256-N260-R263 motif of MCL1 via electrostatic and hydrogen bonding interactions. Further structural comparisons elucidate the characterization of MCL1 interaction with BH3 ligands. These findings help understand the anti-apoptotic properties of MCL1 and provide new perspectives for designing and optimization of BH3 mimetics.