Repurposing Boswellic Acid Derivatives as Dual-Site Inhibitors of SQLE: Biochemical and Computational Insights

Squalene epoxidase (SQLE), a rate-limiting enzyme in cholesterol biosynthesis and a validated antifungal–anticancer target, was probed with four boswellic-acid derivatives isolated from Boswellia sacra. After purification and NMR-based structure elucidation, the compounds were tested in vitro, revealing that 9,11-dehydro-β-boswellic acid and its acetyl analogue inhibit SQLE with low-micromolar IC₅₀ values (~2 µM) and non-competitive kinetics, surpassing the reference inhibitor tris-norsqualene cyclopropylamine. Two more heavily substituted analogues were weaker, one acting non-competitively and the other showing mixed-type inhibition with a dominant competitive component. Docking and 200-ns molecular-dynamics simulations showed that the potent Δ⁹,¹¹ scaffold targets an allosteric vestibule defined by Ser531/Gln500, whereas the mixed inhibitor occupies the FAD entrance channel. Free-energy-landscape mapping and MM/PBSA calculations confirmed that the allosteric complexes display the deepest energetic minima and most favorable binding enthalpies (≈ –24 kcal mol⁻¹), while dynamic descriptors (RMSD, RMSF, Rg, SASA, hydrogen bonding, and interaction energies) indicated that ligand binding leaves the global fold intact but stabilizes local loops. In silico ADMET profiling suggested acceptable drug-likeness, low hERG and CNS liabilities, and manageable CYP2C9 interaction for the Δ⁹,¹¹ derivatives, although extremely low aqueous solubility and moderate genotoxic alerts remain hurdles for optimization. Collectively, these findings establish boswellic acids—particularly the 9,11-dehydro core—as promising natural allosteric modulators of SQLE and illustrate a streamlined phytochemical-biochemical-computational workflow for repurposing natural products against challenging enzymatic targets.