Structure-Based Design and Structure-Activity Relationship Analysis of Small Molecules Inhibiting Bcl-2 Family Members

Based on a Mcl-1/Bcl-2 dual inhibitor (S1) previously reported by our group, structure-directed molecular design and structure-activity relationship (SAR) analysis were performed to investigate structural features contributing to the Mcl-1/Bcl-2 binding selectivity and affinity. A series of S1 derivatives with various pharmacophores were synthesized, and among these a selective Mcl-1 inhibitor A4 with 5-fold selectivity over Bcl-2 (Ki = 0.37 ± 0.07 μM vs. 1.87 ± 0.21 μM) and a dual Mcl-1/Bcl-2 inhibitor B3 with optimized affinities (Ki = 0.35 ± 0.01 μM for Mcl-1 and 0.81 ± 0.01 μM for Bcl-2) were revealed by fluorescence polarization assay (FPA). The SAR data and binding modes of A4 and B3 examined by molecular docking showed that the p1 pocket having different geometry and binding features between Mcl-1 and Bcl-2 contributed to the specific binding properties of Mcl-1, and the spatial conserved N223 on Mcl-1 and N143 on Bcl-2 were the key residues to form additional hydrogen bonds with the ester of B3. Finally, the apoptosis-inducing potencies of A4 and B3 in the μM range against K562 and MCF-7 cancer cells were consistent with their binding selectivity determined in vitro, and only weak killing was found for these compounds in the normal cells.