Study of Binding Thermodynamics in the Optimization of BH3 Mimetics

The use of small molecule B‐cell lymphoma 2 homology domain 3 mimetics to neutralize the B‐cell lymphoma 2 protein is an attractive strategy for cancer treatment due to its ability to cause targeted cell apoptosis. We have previously reported the design and optimization of a series of B‐cell lymphoma 2 homology domain 3‐mimetics, called compounds 1 – 6 . In this study, we evaluated the optimization of B‐cell lymphoma 2 homology domain 3‐mimetics from a thermodynamic perspective. Understanding the thermodynamic parameters of B‐cell lymphoma 2 homology domain 3‐mimetics plays a critical role in the development of B‐cell lymphoma 2 small‐molecule inhibitors. The thermodynamic parameters for the interactions of these compounds with the myeloid cell leukemia sequence 1 protein were obtained using isothermal titration calorimetry. Owing to compounds 1 – 6 overcoming enthalpy–entropy compensation, the affinities of them improved gradually. Toward binding to the myeloid cell leukemia sequence 1 protein, compound 6 was deemed optimal with an obtained K_d value of 238 nm , which is a 10⁴‐fold improvement compared with 1 . Analysis of the enthalpy and ?TΔS efficiencies showed that ligand efficiencies with respect to molecular size are correlated with the enthalpic efficiencies. Notably, an enthalpy gain of 4.65 kcal/mol identified that an additional hydrogen bond is formed by 2 with myeloid cell leukemia sequence 1 compared with compound 1 . For the first time, hydrogen bonding between a small‐molecule inhibitor of B‐cell lymphoma 2 was demonstrated experimentally.