Investigating the binding mechanism of AML inhibitors based on panobinostat with HDAC3 proteins using Gaussian accelerated molecular dynamics

Class I histone deacetylases (HDACs) play a crucial role in the transformation and survival of myeloid and lymphoid malignancies, with HDAC1, 2, and 3 (Class I HDACs) being potential molecular targets for acute myelogenous leukemia (AML) treatment. Among them, HDAC3 depletion or inhibition significantly reduces proliferation and promotes differentiation in leukemia, with inhibitors like Panobinostat and compound 13a showing promise in suppressing its activity. In this study, we utilized Gaussian accelerated molecular dynamics (GaMD) simulations to compare the inhibitory potency of 13a and Panobinostat against HDAC3. Our findings suggest that the superior inhibitory activity of 13a may be attributed to its stronger interactions with HDAC3. Distance analysis demonstrated that 13a maintains a closer and more consistent coordination with the zinc ion in the catalytic pocket, resulting in a more stable interaction compared to Panobinostat. Additionally, interaction analysis revealed that 13a forms more π-alkyl interactions, along with additional attractive charge and metal-acceptor interactions with HDAC3. Principal component analysis (PCA) further showed that the binding of 13a stabilizes HDAC3 in multiple distinct conformational states, suggesting that a more substantial conformational rearrangement is required upon 13a binding. This structural complexity may explain why 13a behaves as a slow-on/slow-off inhibitor and exhibits a superior IC₅₀ compared to Panobinostat. Alanine scanning identified residues such as PRO23, HIS125, and PHE144 as potential sites for inhibitor binding, making significant contributions to binding affinity. These combined findings suggest that 13a not only has a higher inhibitory potency but also holds potential for further optimization, making it a promising candidate for targeted cancer therapy.