Computational Investigation of Structural Basis for Enhanced Binding of Isoflavone Analogues with Mitochondrial Aldehyde Dehydrogenase

[Image: see text] Isoflavone compounds are potent inhibitors against mitochondrial aldehyde dehydrogenase (ALDH2) for the treatment of alcoholism and drug addiction, and an in-depth understanding of the underlying structural basis helps design new inhibitors for enhanced binding. Here, we investigated the binding poses and strengths of eight isoflavone analogues (including CVT-10216 and daidzin) with ALDH2 via computational methods of molecular docking, molecular dynamics (MD) simulation, molecular mechanics Poisson–Boltzmann surface area (MM-PBSA), steered MD, and umbrella sampling. Neither the Vina scoring of docked and MD-sampled complexes nor the nonbonded protein–inhibitor interaction energy from MD simulations is able to reproduce the relative binding strength of the inhibitors compared to experimental IC(50) values. Considering the solvation contribution, MM-PBSA and relatively expensive umbrella sampling yield good performance for the relative binding (free) energies. The isoflavone skeleton prefers to form π–π stacking, π–sulfur, and π–alkyl interactions with planar (Phe and Trp) or sulfur-containing (Cys and Met) residues. The enhanced inhibition of CVT-10216 originates from both end groups of the isoflavone skeleton offering strong van der Waals contacts and from the methylsulfonamide group at the 4′ position by hydrogen bonding (HB) with neighboring receptor residues. These results indicate that the hydrophobic binding tunnel of ALDH2 is larger than the isoflavone skeleton in length and thus an extended hydrophobic core is likely a premise for potent inhibitors.