Thermodynamic Preference Between Deprotonation Pathways in Boronic Acid-Based Proteasome Inhibitors: Insights from a...

Background/Objectives: Boronic acid-based proteasome inhibitors (BABPIs) including Bortezomib, Ixazomib, and Delanzomib are clinically relevant anticancer agents whose mechanism of action depends on direct interaction between the boronic acid warhead and the threonine residue at the first position (Thr1), leading to the formation of covalent tetrahedral complex. Although the formation of this complex is well studied, the subsequent behavior of the boronic acid warhead, particularly the possible formation of monoanionic boronate species through deprotonation of one of the two boronic hydroxyl groups, remains unexplored. Therefore, the present study addresses whether the formation of Thr1-OH and a monoanionic boronate species is thermodynamically favorable and which of the two hydroxyl groups is more favorable for deprotonation. Methods: Density Functional Theory (DFT) calculations at the B3LYP/6-311+G(d,p) level, combined with the Polarizable Continuum Model (PCM), were used to study two competing deprotonation pathways for the inhibitors and for a simplified warhead model. To mimic the proteasome environment, reactions were modeled in different polar media-diethyl ether (ε = 4), methanol (ε = 33), and water (ε = 78). Results: Our DFT calculations confirmed that the covalent tetrahedral complex could convert into Thr1-OH and a monoanionic boronate species, representing the deprotonation of one of the boronic hydroxyl groups. Deprotonation via pathway 1 is more favorable than deprotonation via pathway 2 for all inhibitors, especially in polar solvents. Bortezomib demonstrated a strong preference for -OH₁ deprotonation with ∆∆G ≈ -7 kcal·mol^-1. In contrast, Ixazomib, Delanzomib, and the simplified warhead model showed smaller ∆∆G values (≈-2 kcal·mol^-1), within the method's uncertainty (±2 kcal·mol^-1), suggesting both deprotonation modes under physiological conditions. Conclusions: These results provide comparative thermodynamic insight into the deprotonation behavior of BABPIs, suggesting that the two hydroxyl groups are not equivalent during deprotonation. This finding offers a physicochemical framework that may support the rational design of next-generation BABPIs.